############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mzR_2.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mzR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mzR.buildbin-libdir mzR_2.39.0.tar.gz' >>>>>>> * installing *source* package ‘mzR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ rm -f 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/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_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/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.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/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/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) RcppPwiz.cpp:408:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans); ~~ ^~~~~~~ %zu RcppPwiz.cpp:778:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if ( (precursorScanNum[i] > 0) | (precursorMZ[i] > 0) ) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || RcppPwiz.cpp:778:10: note: cast one or both operands to int to silence this warning RcppPwiz.cpp:854:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1); ~~ ^~~~~~~~~~~~~~~ %zu 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from RcppPwizModule.cpp:2: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:30: In file included from ./pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from RcppIdent.cpp:1: In file included from ./RcppIdent.h:14: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from RcppIdent.cpp:1: In file included from ./RcppIdent.h:14: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from RcppIdentModule.cpp:2: In file included from ./RcppIdent.h:14: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from RcppIdentModule.cpp:2: In file included from ./RcppIdent.h:14: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o In file included from pwiz/data/common/MemoryIndex.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/MemoryIndex.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/MemoryIndex.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/MemoryIndex.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/MemoryIndex.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/detail/shared_count.hpp:27: In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27: In file included from ./boost/checked_delete.hpp:15: ./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::MemoryIndex::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ ./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ ./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ ./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' 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::shared_ptr' requested here PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {} ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o In file included from pwiz/data/common/CVTranslator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/CVTranslator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/CVTranslator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/CVTranslator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/CVTranslator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/common/CVTranslator.cpp:145:53: warning: '&&' within '||' [-Wlogical-op-parentheses] return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ~~ pwiz/data/common/CVTranslator.cpp:145:53: 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:146:40: 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:146:40: 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:147:40: warning: '&&' within '||' [-Wlogical-op-parentheses] key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:147:40: 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:148:40: warning: '&&' within '||' [-Wlogical-op-parentheses] key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:148:40: note: place parentheses around the '&&' expression to silence this warning key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ^ ( ) 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o In file included from pwiz/data/common/cv.cpp:34: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/cv.cpp:34: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/cv.cpp:34: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/cv.cpp:34: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/cv.cpp:34: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o In file included from pwiz/data/common/ParamTypes.cpp:26: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/ParamTypes.cpp:26: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/ParamTypes.cpp:26: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/ParamTypes.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/ParamTypes.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o In file included from pwiz/data/common/BinaryIndexStream.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/BinaryIndexStream.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/BinaryIndexStream.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/BinaryIndexStream.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/BinaryIndexStream.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/shared_ptr.hpp:17: In file included from ./boost/smart_ptr/detail/shared_count.hpp:27: In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27: In file included from ./boost/checked_delete.hpp:15: ./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::BinaryIndexStream::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ ./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ ./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ ./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ pwiz/data/common/BinaryIndexStream.cpp:417:82: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr isPtr) : impl_(new Impl(isPtr)) {} ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o In file included from pwiz/data/common/diff_std.cpp:26: In file included from pwiz/data/common/diff_std.hpp:33: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/diff_std.cpp:26: In file included from pwiz/data/common/diff_std.hpp:33: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/diff_std.cpp:26: In file included from pwiz/data/common/diff_std.hpp:33: In file included from pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/diff_std.cpp:27: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/diff_std.cpp:27: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:19: In file included from ./boost_aux/boost/enum/base.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:19: In file included from ./boost_aux/boost/enum/base.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:20: In file included from ./boost_aux/boost/enum/bitfield.hpp:22: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:20: In file included from ./boost_aux/boost/enum/bitfield.hpp:22: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/common/Unimod.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:20: In file included from ./boost_aux/boost/enum/bitfield.hpp:22: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const std::basic_string &, boost::algorithm::detail::token_finderF>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/common/Unimod.cpp:131:22: note: in instantiation of function template specialization 'boost::algorithm::split>, const std::basic_string &, boost::algorithm::detail::is_classifiedF>' requested here bal::split(formulaTokens, itr->second, bal::is_space()); ^ In file included from pwiz/data/common/Unimod.cpp:25: In file included from pwiz/data/common/Unimod.hpp:31: In file included from ./boost_aux/boost/enum.hpp:20: In file included from ./boost_aux/boost/enum/bitfield.hpp:22: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const std::basic_string &, boost::algorithm::detail::token_finderF>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/common/Unimod.cpp:131:22: note: in instantiation of function template specialization 'boost::algorithm::split>, const std::basic_string &, boost::algorithm::detail::is_classifiedF>' requested here bal::split(formulaTokens, itr->second, bal::is_space()); ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/../MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/../MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:27: In file included from pwiz/data/msdata/mz5/../MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/mz5/../Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from pwiz/data/msdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/DefaultReaderList.cpp:29: In file included from pwiz/data/msdata/DefaultReaderList.hpp:29: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o In file included from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: In file included from pwiz/data/msdata/ChromatogramList_mzML.hpp:29: In file included from pwiz/data/msdata/ChromatogramListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: In file included from pwiz/data/msdata/ChromatogramList_mzML.hpp:29: In file included from pwiz/data/msdata/ChromatogramListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: In file included from pwiz/data/msdata/ChromatogramList_mzML.hpp:29: In file included from pwiz/data/msdata/ChromatogramListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/ChromatogramList_mz5.cpp:28: In file included from pwiz/data/msdata/ChromatogramList_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o In file included from pwiz/data/msdata/examples.cpp:25: In file included from pwiz/data/msdata/examples.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/examples.cpp:25: In file included from pwiz/data/msdata/examples.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/examples.cpp:25: In file included from pwiz/data/msdata/examples.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/examples.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/examples.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from pwiz/data/msdata/Serializer_mzML.cpp:26: In file included from pwiz/data/msdata/Serializer_mzML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Serializer_mzML.cpp:26: In file included from pwiz/data/msdata/Serializer_mzML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Serializer_mzML.cpp:26: In file included from pwiz/data/msdata/Serializer_mzML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Serializer_mzML.cpp:28: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_mzML.cpp:28: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from pwiz/data/msdata/Serializer_MSn.cpp:25: In file included from pwiz/data/msdata/Serializer_MSn.hpp:26: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Serializer_MSn.cpp:25: In file included from pwiz/data/msdata/Serializer_MSn.hpp:26: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Serializer_MSn.cpp:25: In file included from pwiz/data/msdata/Serializer_MSn.hpp:26: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Serializer_MSn.cpp:25: In file included from pwiz/data/msdata/Serializer_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_MSn.cpp:25: In file included from pwiz/data/msdata/Serializer_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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; } ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Reader.cpp:26: In file included from pwiz/data/msdata/Reader.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from pwiz/data/msdata/Serializer_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Serializer_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Serializer_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Serializer_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/Serializer_mz5.cpp:28: In file included from pwiz/data/msdata/Serializer_mz5.hpp:32: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from pwiz/data/msdata/Serializer_MGF.cpp:25: In file included from pwiz/data/msdata/Serializer_MGF.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:25: In file included from pwiz/data/msdata/Serializer_MGF.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:25: In file included from pwiz/data/msdata/Serializer_MGF.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:29: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:13: In file included from ./boost/spirit/home/karma/char.hpp:13: In file included from ./boost/spirit/home/karma/char/char.hpp:15: In file included from ./boost/spirit/home/support/string_traits.hpp:16: In file included from ./boost/spirit/home/support/container.hpp:21: In file included from ./boost/variant.hpp:17: In file included from ./boost/variant/variant.hpp:30: In file included from ./boost/variant/detail/initializer.hpp:21: In file included from ./boost/detail/reference_content.hpp:19: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here : T::type ^ ./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_>' requested here : T::type ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:25:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T1)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>, mpl_::bool_, mpl_::bool_, mpl_::bool_>' requested here : aux::and_impl< ^ ./boost/mpl/iter_fold_if.hpp:42:11: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) : and_< ^ ./boost/mpl/iter_fold_if.hpp:85:9: note: in instantiation of template class 'boost::mpl::aux::iter_fold_if_impl, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect, boost::mpl::l_iter>>, mpl_::na, boost::mpl::always>>' requested here aux::iter_fold_if_impl< ^ ./boost/mpl/iter_fold_if.hpp:102:20: note: in instantiation of member class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>::result_' requested here typename result_::state ^ ./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>' requested here typedef typename mpl::iter_fold_if< ^ ./boost/variant/variant.hpp:1250:39: note: in instantiation of template class 'boost::detail::variant::find_fallback_type, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>' requested here typedef typename detail::variant::find_fallback_type< ^ ./boost/spirit/home/support/info.hpp:69:20: note: in instantiation of template class 'boost::variant, boost::recursive_wrapper, boost::recursive_wrapper>, boost::recursive_wrapper>>' requested here value_type value; ^ In file included from pwiz/data/msdata/Serializer_MGF.cpp:29: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:21: In file included from ./boost/spirit/home/karma/binary.hpp:13: In file included from ./boost/spirit/home/karma/binary/binary.hpp:15: In file included from ./boost/spirit/home/support/detail/endian.hpp:19: In file included from ./boost/endian/arithmetic.hpp:30: In file included from ./boost/endian/buffers.hpp:30: In file included from ./boost/endian/detail/endian_store.hpp:12: In file included from ./boost/endian/detail/is_trivially_copyable.hpp:11: ./boost/type_traits/has_trivial_assign.hpp:29:7: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value && is_assignable::value) ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from pwiz/data/msdata/Serializer_mzXML.cpp:25: In file included from pwiz/data/msdata/Serializer_mzXML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Serializer_mzXML.cpp:25: In file included from pwiz/data/msdata/Serializer_mzXML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Serializer_mzXML.cpp:25: In file included from pwiz/data/msdata/Serializer_mzXML.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Serializer_mzXML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Serializer_mzXML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumListBase.cpp:25: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ ./boost/type_traits/has_trivial_constructor.hpp:51:68: note: in instantiation of template class 'boost::has_trivial_constructor, std::basic_string>>>' requested here template struct has_trivial_default_constructor : public has_trivial_constructor {}; ^ ./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor, std::basic_string>>>' requested here BOOST_MPL_AUX_STATIC_CAST(bool, BOOST_MPL_AUX_VALUE_WKND(T1)::value) ^ ./boost/range/detail/default_constructible_unary_fn.hpp:71:34: note: in instantiation of template class 'boost::mpl::if_, std::basic_string>>>, boost::range_detail::select_first, std::basic_string>>, boost::range_detail::default_constructible_unary_fn_wrapper, std::basic_string>>, const std::basic_string &>>' requested here typedef typename boost::mpl::if_< ^ ./boost/range/adaptor/transformed.hpp:31:26: note: in instantiation of template class 'boost::range_detail::default_constructible_unary_fn_gen, std::basic_string>>, const std::basic_string &>' requested here typename default_constructible_unary_fn_gen< ^ ./boost/range/adaptor/transformed.hpp:42:26: note: in instantiation of template class 'boost::range_detail::transform_iterator_gen, std::basic_string>>, std::__map_const_iterator, std::basic_string>, std::__tree_node, std::basic_string>, void *> *, long>>>' requested here typename transform_iterator_gen< ^ ./boost/range/adaptor/map.hpp:65:22: note: in instantiation of template class 'boost::range_detail::transformed_range, std::basic_string>>, const std::map, std::basic_string>>' requested here : public transformed_range< ^ pwiz/data/msdata/SpectrumListBase.cpp:62:38: note: in instantiation of template class 'boost::range_detail::select_first_range, std::basic_string>>' requested here auto actualIdKeys = actualId | boost::adaptors::map_keys; ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/SpectrumList_MGF.cpp:243:38: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here bal::split(charges, value, bal::is_any_of(" ")); ^ In file included from pwiz/data/msdata/SpectrumList_MGF.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MGF.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/SpectrumList_MGF.cpp:243:38: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here bal::split(charges, value, bal::is_any_of(" ")); ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:26: In file included from pwiz/data/msdata/SpectrumList_mzML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:31: ./boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ ./boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :290:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o In file included from pwiz/data/msdata/SpectrumList_MSn.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_MSn.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_MSn.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_MSn.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_MSn.cpp:26: In file included from pwiz/data/msdata/SpectrumList_MSn.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/msdata/SpectrumList_MSn.cpp:641:12: warning: variable 'lineCount' set but not used [-Wunused-but-set-variable] size_t lineCount = 0; ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumList_mz5.cpp:28: In file included from pwiz/data/msdata/SpectrumList_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31: In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28: In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:38: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:38: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:38: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:38: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:38: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o In file included from pwiz/data/msdata/Diff.cpp:26: In file included from pwiz/data/msdata/Diff.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Diff.cpp:26: In file included from pwiz/data/msdata/Diff.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Diff.cpp:26: In file included from pwiz/data/msdata/Diff.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Diff.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Diff.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o In file included from pwiz/data/msdata/MSData.cpp:25: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/MSData.cpp:25: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/MSData.cpp:25: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/MSData.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/MSData.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/msdata/MSData.cpp:1115:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ In file included from pwiz/data/msdata/MSData.cpp:25: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/MSData.cpp:508:12: note: in instantiation of function template specialization 'boost::algorithm::split>, const std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here boost::split(pairs, id, boost::is_any_of(" \t\n\r")); ^ In file included from pwiz/data/msdata/MSData.cpp:25: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/MSData.cpp:508:12: note: in instantiation of function template specialization 'boost::algorithm::split>, const std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here boost::split(pairs, id, boost::is_any_of(" \t\n\r")); ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o In file included from pwiz/data/msdata/References.cpp:25: In file included from pwiz/data/msdata/References.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/References.cpp:25: In file included from pwiz/data/msdata/References.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/References.cpp:25: In file included from pwiz/data/msdata/References.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/References.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/References.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/SpectrumList_mzXML.cpp:163:35: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here boost::algorithm::split(strCharges, possibleCharges, boost::is_any_of(",")); ^ In file included from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: In file included from pwiz/data/msdata/SpectrumList_mzXML.hpp:29: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/msdata/SpectrumList_mzXML.cpp:163:35: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here boost::algorithm::split(strCharges, possibleCharges, boost::is_any_of(",")); ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o In file included from pwiz/data/msdata/IO.cpp:26: In file included from pwiz/data/msdata/IO.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/IO.cpp:26: In file included from pwiz/data/msdata/IO.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/IO.cpp:26: In file included from pwiz/data/msdata/IO.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/IO.cpp:29: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/IO.cpp:29: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/msdata/IO.cpp:2132:35: warning: '&&' within '||' [-Wlogical-op-parentheses] else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/IO.cpp:2132:35: 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:2836:31: warning: '&&' within '||' [-Wlogical-op-parentheses] else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ pwiz/data/msdata/IO.cpp:2836:31: note: place parentheses around the '&&' expression to silence this warning else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ^ ( ) 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: In file included from pwiz/data/msdata/SpectrumList_BTDX.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: In file included from pwiz/data/msdata/SpectrumList_BTDX.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: In file included from pwiz/data/msdata/SpectrumList_BTDX.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:28: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: In file included from pwiz/data/msdata/SpectrumList_BTDX.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: In file included from pwiz/data/msdata/SpectrumList_BTDX.hpp:30: In file included from pwiz/data/msdata/SpectrumListBase.hpp:31: In file included from ./boost/range/adaptor/map.hpp:14: In file included from ./boost/range/adaptor/transformed.hpp:15: In file included from ./boost/range/detail/default_constructible_unary_fn.hpp:13: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/msdata/SpectrumList_BTDX.cpp:279:19: warning: private field 'msd_' is not used [-Wunused-private-field] const MSData& msd_; ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o In file included from pwiz/data/msdata/SpectrumInfo.cpp:27: In file included from pwiz/data/msdata/SpectrumInfo.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumInfo.cpp:27: In file included from pwiz/data/msdata/SpectrumInfo.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumInfo.cpp:27: In file included from pwiz/data/msdata/SpectrumInfo.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumInfo.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumInfo.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o In file included from pwiz/data/msdata/LegacyAdapter.cpp:27: In file included from pwiz/data/msdata/LegacyAdapter.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:27: In file included from pwiz/data/msdata/LegacyAdapter.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:27: In file included from pwiz/data/msdata/LegacyAdapter.hpp:30: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:29: In file included from ./boost/lambda/lambda.hpp:14: In file included from ./boost/lambda/core.hpp:48: In file included from ./boost/lambda/detail/lambda_traits.hpp:18: In file included from ./boost/type_traits/object_traits.hpp:17: ./boost/type_traits/has_trivial_assign.hpp:29:7: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:29: In file included from ./boost/lambda/lambda.hpp:14: In file included from ./boost/lambda/core.hpp:48: In file included from ./boost/lambda/detail/lambda_traits.hpp:18: In file included from ./boost/type_traits/object_traits.hpp:21: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:29: In file included from ./boost/lambda/lambda.hpp:14: In file included from ./boost/lambda/core.hpp:48: In file included from ./boost/lambda/detail/lambda_traits.hpp:18: In file included from ./boost/type_traits/object_traits.hpp:22: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/data/msdata/LegacyAdapter.cpp:29: In file included from ./boost/lambda/lambda.hpp:14: In file included from ./boost/lambda/core.hpp:48: In file included from ./boost/lambda/detail/lambda_traits.hpp:18: In file included from ./boost/type_traits/object_traits.hpp:23: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o In file included from pwiz/data/msdata/SpectrumIterator.cpp:26: In file included from pwiz/data/msdata/SpectrumIterator.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumIterator.cpp:26: In file included from pwiz/data/msdata/SpectrumIterator.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumIterator.cpp:26: In file included from pwiz/data/msdata/SpectrumIterator.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumIterator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumIterator.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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() || ^ ( ) 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:29: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/MSDataFile.cpp:26: In file included from pwiz/data/msdata/MSDataFile.hpp:30: In file included from pwiz/data/msdata/Reader.hpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses] mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; ^ ( ) 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:27: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:28: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:29: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:30: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:30: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_copy_constructor' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:39:54: note: expanded from macro 'BOOST_STRONG_TYPEDEF' explicit D(const T& t_) BOOST_NOEXCEPT_IF(boost::has_nothrow_copy_constructor::value) : t(t_) {} \ ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:29: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/type_traits/has_nothrow_constructor.hpp:69:68: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here template struct has_nothrow_default_constructor : public has_nothrow_constructor{}; ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_default_constructor' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:40:34: note: expanded from macro 'BOOST_STRONG_TYPEDEF' D() BOOST_NOEXCEPT_IF(boost::has_nothrow_default_constructor::value) : t() {} \ ^ In file included from pwiz/data/msdata/SpectrumListCache.cpp:25: In file included from pwiz/data/msdata/SpectrumListCache.hpp:28: In file included from pwiz/data/msdata/MemoryMRUCache.hpp:27: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:28: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_assign' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:42:57: note: expanded from macro 'BOOST_STRONG_TYPEDEF' D& operator=(const D& rhs) BOOST_NOEXCEPT_IF(boost::has_nothrow_assign::value) {t = rhs.t; return *this;} \ ^ 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o In file included from pwiz/data/msdata/Index_mzML.cpp:24: In file included from pwiz/data/msdata/Index_mzML.hpp:28: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/Index_mzML.cpp:24: In file included from pwiz/data/msdata/Index_mzML.hpp:28: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/Index_mzML.cpp:24: In file included from pwiz/data/msdata/Index_mzML.hpp:28: In file included from pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/Index_mzML.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/Index_mzML.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:30: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:30: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:30: In file included from ./pwiz/utility/misc/mru_list.hpp:25: In file included from ./boost/multi_index_container.hpp:36: In file included from ./boost/multi_index/detail/base_type.hpp:21: In file included from ./boost/multi_index/detail/index_base.hpp:33: In file included from ./boost/multi_index/detail/index_loader.hpp:22: In file included from ./boost/serialization/nvp.hpp:35: In file included from ./boost/serialization/split_free.hpp:22: In file included from ./boost/serialization/serialization.hpp:14: In file included from ./boost/serialization/strong_typedef.hpp:30: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_copy_constructor' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:39:54: note: expanded from macro 'BOOST_STRONG_TYPEDEF' explicit D(const T& t_) BOOST_NOEXCEPT_IF(boost::has_nothrow_copy_constructor::value) : t(t_) {} \ ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/type_traits/has_nothrow_constructor.hpp:69:68: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here template struct has_nothrow_default_constructor : public has_nothrow_constructor{}; ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_default_constructor' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:40:34: note: expanded from macro 'BOOST_STRONG_TYPEDEF' D() BOOST_NOEXCEPT_IF(boost::has_nothrow_default_constructor::value) : t() {} \ ^ In file included from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ ./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_assign' requested here BOOST_STRONG_TYPEDEF(unsigned int, version_type) ^ ./boost/serialization/strong_typedef.hpp:42:57: note: expanded from macro 'BOOST_STRONG_TYPEDEF' D& operator=(const D& rhs) BOOST_NOEXCEPT_IF(boost::has_nothrow_assign::value) {t = rhs.t; return *this;} \ ^ 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/IdentDataFile.cpp:30: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/IdentDataFile.cpp:30: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o In file included from pwiz/data/identdata/IdentData.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/identdata/IdentData.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/identdata/IdentData.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/IdentData.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/IdentData.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o In file included from pwiz/data/identdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/identdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/identdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/DefaultReaderList.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/Reader.cpp:27: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/Reader.cpp:27: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/Serializer_protXML.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/Serializer_protXML.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder-ctor] strict(strict), ^~~~~~~~~~~~~~ SourceFilesPtr(returnValueSourceFiles) 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; ^ 9 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/Serializer_pepXML.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/Serializer_pepXML.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ ./boost/type_traits/has_trivial_constructor.hpp:51:68: note: in instantiation of template class 'boost::has_trivial_constructor' requested here template struct has_trivial_default_constructor : public has_trivial_constructor {}; ^ ./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor' requested here BOOST_MPL_AUX_STATIC_CAST(bool, BOOST_MPL_AUX_VALUE_WKND(T1)::value) ^ ./boost/range/detail/default_constructible_unary_fn.hpp:71:34: note: in instantiation of template class 'boost::mpl::if_, pwiz::identdata::(anonymous namespace)::EnzymePtr_name, boost::range_detail::default_constructible_unary_fn_wrapper>>' requested here typedef typename boost::mpl::if_< ^ ./boost/range/adaptor/transformed.hpp:31:26: note: in instantiation of template class 'boost::range_detail::default_constructible_unary_fn_gen>' requested here typename default_constructible_unary_fn_gen< ^ ./boost/range/adaptor/transformed.hpp:42:26: note: in instantiation of template class 'boost::range_detail::transform_iterator_gen *>>' requested here typename transform_iterator_gen< ^ pwiz/data/identdata/Serializer_pepXML.cpp:415:55: note: in instantiation of template class 'boost::range_detail::transformed_range>>' requested here string enzymeName = bal::join(sip.enzymes.enzymes | boost::adaptors::transformed(EnzymePtr_name()), " + "); ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ ./boost/type_traits/has_trivial_constructor.hpp:51:68: note: in instantiation of template class 'boost::has_trivial_constructor' requested here template struct has_trivial_default_constructor : public has_trivial_constructor {}; ^ ./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor' requested here BOOST_MPL_AUX_STATIC_CAST(bool, BOOST_MPL_AUX_VALUE_WKND(T1)::value) ^ ./boost/range/detail/default_constructible_unary_fn.hpp:71:34: note: in instantiation of template class 'boost::mpl::if_, pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, boost::range_detail::default_constructible_unary_fn_wrapper>' requested here typedef typename boost::mpl::if_< ^ ./boost/range/adaptor/transformed.hpp:31:26: note: in instantiation of template class 'boost::range_detail::default_constructible_unary_fn_gen' requested here typename default_constructible_unary_fn_gen< ^ ./boost/range/adaptor/transformed.hpp:42:26: note: in instantiation of template class 'boost::range_detail::transform_iterator_gen *>>' requested here typename transform_iterator_gen< ^ pwiz/data/identdata/Serializer_pepXML.cpp:418:73: note: in instantiation of template class 'boost::range_detail::transformed_range>>' requested here int minSpecificity = *boost::range::min_element(sip.enzymes.enzymes | boost::adaptors::transformed(EnzymePtr_specificity())); ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ ./boost/type_traits/has_trivial_constructor.hpp:51:68: note: in instantiation of template class 'boost::has_trivial_constructor' requested here template struct has_trivial_default_constructor : public has_trivial_constructor {}; ^ ./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor' requested here BOOST_MPL_AUX_STATIC_CAST(bool, BOOST_MPL_AUX_VALUE_WKND(T1)::value) ^ ./boost/range/detail/default_constructible_unary_fn.hpp:71:34: note: in instantiation of template class 'boost::mpl::if_, pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, boost::range_detail::default_constructible_unary_fn_wrapper>' requested here typedef typename boost::mpl::if_< ^ ./boost/range/adaptor/transformed.hpp:31:26: note: in instantiation of template class 'boost::range_detail::default_constructible_unary_fn_gen' requested here typename default_constructible_unary_fn_gen< ^ ./boost/range/adaptor/transformed.hpp:42:26: note: in instantiation of template class 'boost::range_detail::transform_iterator_gen *>>' requested here typename transform_iterator_gen< ^ pwiz/data/identdata/Serializer_pepXML.cpp:504:81: note: in instantiation of template class 'boost::range_detail::transformed_range>>' requested here int maxMissedCleavages = *boost::range::max_element(sip.enzymes.enzymes | boost::adaptors::transformed(EnzymePtr_missedCleavages())); ^ 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); ^ & [ ] 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ ./boost/type_traits/has_trivial_constructor.hpp:51:68: note: in instantiation of template class 'boost::has_trivial_constructor' requested here template struct has_trivial_default_constructor : public has_trivial_constructor {}; ^ ./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor' requested here BOOST_MPL_AUX_STATIC_CAST(bool, BOOST_MPL_AUX_VALUE_WKND(T1)::value) ^ ./boost/range/detail/default_constructible_unary_fn.hpp:71:34: note: in instantiation of template class 'boost::mpl::if_, pwiz::identdata::(anonymous namespace)::CVParam_name, boost::range_detail::default_constructible_unary_fn_wrapper>>' requested here typedef typename boost::mpl::if_< ^ ./boost/range/adaptor/transformed.hpp:31:26: note: in instantiation of template class 'boost::range_detail::default_constructible_unary_fn_gen>' requested here typename default_constructible_unary_fn_gen< ^ ./boost/range/adaptor/transformed.hpp:42:26: note: in instantiation of template class 'boost::range_detail::transform_iterator_gen>' requested here typename transform_iterator_gen< ^ pwiz/data/identdata/Serializer_pepXML.cpp:586:65: note: in instantiation of template class 'boost::range_detail::transformed_range>' requested here string description = bal::join(possibleMods | boost::adaptors::transformed(CVParam_name()), ", "); ^ pwiz/data/identdata/Serializer_pepXML.cpp:1546:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2, const char *, const char *>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2, const char *, const char *>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const char *const &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/identdata/Serializer_pepXML.cpp:113:18: note: in instantiation of function template specialization 'boost::algorithm::split>, const char *const &, boost::algorithm::detail::is_any_ofF>' requested here bal::split(names, ast.softwareNames, bal::is_any_of(";")); ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2, const char *, const char *>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2, const char *, const char *>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, const char *const &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/identdata/Serializer_pepXML.cpp:113:18: note: in instantiation of function template specialization 'boost::algorithm::split>, const char *const &, boost::algorithm::detail::is_any_ofF>' requested here bal::split(names, ast.softwareNames, bal::is_any_of(";")); ^ pwiz/data/identdata/Serializer_pepXML.cpp:995:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1450:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1796:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field] const CVTranslator& _cvTranslator; ^ pwiz/data/identdata/Serializer_pepXML.cpp:1970:38: warning: private field 'ilr' is not used [-Wunused-private-field] const IterationListenerRegistry* ilr; ^ 18 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/Serializer_mzid.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/Serializer_mzid.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/IO.cpp:30: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/IO.cpp:30: In file included from ./pwiz/utility/misc/Filesystem.hpp:34: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ 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:31: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/References.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/References.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] BOOST_FOREACH(OrganizationPtr& org, static_cast(c.get())->affiliations) ^ ./boost/foreach.hpp:1107:108: note: expanded from macro 'BOOST_FOREACH' if (boost::foreach_detail_::auto_any_t BOOST_FOREACH_ID(_foreach_col) = BOOST_FOREACH_CONTAIN(COL)) {} else \ ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o In file included from pwiz/data/identdata/MascotReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/identdata/MascotReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/identdata/MascotReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/identdata/MascotReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/identdata/MascotReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& 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; ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ In file included from pwiz/data/proteome/Modification.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/proteome/Modification.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/proteome/Modification.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/proteome/Modification.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/proteome/Modification.cpp:30: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr formula_; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy, boost::algorithm::is_equal>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor, boost::algorithm::is_equal>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to, boost::algorithm::is_equal>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2, boost::algorithm::is_equal>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:98:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base, boost::algorithm::is_equal>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:104:21: note: in instantiation of function template specialization 'boost::algorithm::find_iterator>::find_iterator, boost::algorithm::is_equal>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:71:40: note: in instantiation of function template specialization 'boost::algorithm::iter_find>>, const std::basic_string &, boost::algorithm::detail::first_finderF, boost::algorithm::is_equal>>' requested here return ::boost::algorithm::iter_find( ^ pwiz/data/proteome/Digestion.cpp:468:14: note: in instantiation of function template specialization 'boost::algorithm::find_all>>, const std::basic_string &, std::basic_string>' requested here bal::find_all(instances, sequence_, peptide.sequence()); ^ In file included from pwiz/data/proteome/Digestion.cpp:32: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor, boost::algorithm::is_equal>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to, boost::algorithm::is_equal>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2, boost::algorithm::is_equal>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:98:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base, boost::algorithm::is_equal>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:104:21: note: in instantiation of function template specialization 'boost::algorithm::find_iterator>::find_iterator, boost::algorithm::is_equal>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:71:40: note: in instantiation of function template specialization 'boost::algorithm::iter_find>>, const std::basic_string &, boost::algorithm::detail::first_finderF, boost::algorithm::is_equal>>' requested here return ::boost::algorithm::iter_find( ^ pwiz/data/proteome/Digestion.cpp:468:14: note: in instantiation of function template specialization 'boost::algorithm::find_all>>, const std::basic_string &, std::basic_string>' requested here bal::find_all(instances, sequence_, peptide.sequence()); ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -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::swap' declared here: type mismatch at 1st parameter ('virtual_map &' (aka 'virtual_map, std::allocator>> &') vs 'ModificationMap &') virtual void swap(virtual_map& x) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ ./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy>>' requested here template struct has_trivial_copy_constructor : public has_trivial_copy{}; ^ ./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor>>' requested here if (boost::has_trivial_copy_constructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/proteome/Peptide.cpp:337:13: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here split(tokens, massStr, bal::is_any_of(",")); ^ In file included from pwiz/data/proteome/Peptide.cpp:31: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ ./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor>>' requested here boost::has_trivial_destructor::value && ^ ./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::assign_to>>' requested here this->assign_to(f); ^ ./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2>, std::__wrap_iter, std::__wrap_iter>::function2>>' requested here m_Finder(Finder) {} ^ ./boost/algorithm/string/find_iterator.hpp:261:17: note: in instantiation of function template specialization 'boost::algorithm::detail::find_iterator_base>::find_iterator_base>>' requested here detail::find_iterator_base(Finder,0), ^ ./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator>::split_iterator>>' requested here find_iterator_type( ::boost::begin(lit_input), InputEnd, Finder ), ^ ./boost/algorithm/string/split.hpp:158:40: note: in instantiation of function template specialization 'boost::algorithm::iter_split>, std::basic_string &, boost::algorithm::detail::token_finderF>>' requested here return ::boost::algorithm::iter_split( ^ pwiz/data/proteome/Peptide.cpp:337:13: note: in instantiation of function template specialization 'boost::algorithm::split>, std::basic_string &, boost::algorithm::detail::is_any_ofF>' requested here split(tokens, massStr, bal::is_any_of(",")); ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o In file included from pwiz/data/proteome/AminoAcid.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/data/proteome/AminoAcid.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/data/proteome/AminoAcid.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/data/proteome/AminoAcid.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/data/proteome/AminoAcid.cpp:27: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o In file included from pwiz/utility/minimxml/XMLWriter.cpp:25: In file included from pwiz/utility/minimxml/XMLWriter.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:25: In file included from pwiz/utility/minimxml/XMLWriter.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:25: In file included from pwiz/utility/minimxml/XMLWriter.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:29: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:13: In file included from ./boost/spirit/home/karma/char.hpp:13: In file included from ./boost/spirit/home/karma/char/char.hpp:15: In file included from ./boost/spirit/home/support/string_traits.hpp:16: In file included from ./boost/spirit/home/support/container.hpp:21: In file included from ./boost/variant.hpp:17: In file included from ./boost/variant/variant.hpp:30: In file included from ./boost/variant/detail/initializer.hpp:21: In file included from ./boost/detail/reference_content.hpp:19: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here : T::type ^ ./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_>' requested here : T::type ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:25:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T1)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>, mpl_::bool_, mpl_::bool_, mpl_::bool_>' requested here : aux::and_impl< ^ ./boost/mpl/iter_fold_if.hpp:42:11: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) : and_< ^ ./boost/mpl/iter_fold_if.hpp:85:9: note: in instantiation of template class 'boost::mpl::aux::iter_fold_if_impl, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect, boost::mpl::l_iter>>, mpl_::na, boost::mpl::always>>' requested here aux::iter_fold_if_impl< ^ ./boost/mpl/iter_fold_if.hpp:102:20: note: in instantiation of member class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>::result_' requested here typename result_::state ^ ./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>' requested here typedef typename mpl::iter_fold_if< ^ ./boost/variant/variant.hpp:1250:39: note: in instantiation of template class 'boost::detail::variant::find_fallback_type, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>' requested here typedef typename detail::variant::find_fallback_type< ^ ./boost/spirit/home/support/info.hpp:69:20: note: in instantiation of template class 'boost::variant, boost::recursive_wrapper, boost::recursive_wrapper>, boost::recursive_wrapper>>' requested here value_type value; ^ In file included from pwiz/utility/minimxml/XMLWriter.cpp:29: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:21: In file included from ./boost/spirit/home/karma/binary.hpp:13: In file included from ./boost/spirit/home/karma/binary/binary.hpp:15: In file included from ./boost/spirit/home/support/detail/endian.hpp:19: In file included from ./boost/endian/arithmetic.hpp:30: In file included from ./boost/endian/buffers.hpp:30: In file included from ./boost/endian/detail/endian_store.hpp:12: In file included from ./boost/endian/detail/is_trivially_copyable.hpp:11: ./boost/type_traits/has_trivial_assign.hpp:29:7: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value && is_assignable::value) ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o In file included from pwiz/utility/minimxml/SAXParser.cpp:28: In file included from pwiz/utility/minimxml/SAXParser.hpp:31: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/minimxml/SAXParser.cpp:28: In file included from pwiz/utility/minimxml/SAXParser.hpp:31: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/minimxml/SAXParser.cpp:28: In file included from pwiz/utility/minimxml/SAXParser.hpp:31: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/minimxml/SAXParser.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/minimxml/SAXParser.cpp:29: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o In file included from pwiz/utility/chemistry/Chemistry.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/chemistry/Chemistry.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/chemistry/Chemistry.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/chemistry/Chemistry.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/chemistry/Chemistry.cpp:28: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o In file included from pwiz/utility/chemistry/MZTolerance.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/chemistry/MZTolerance.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/chemistry/MZTolerance.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/chemistry/MZTolerance.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/chemistry/MZTolerance.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o In file included from pwiz/utility/misc/IntegerSet.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/IntegerSet.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/IntegerSet.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/IntegerSet.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/IntegerSet.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 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()); ^ ( ) 7 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o In file included from pwiz/utility/misc/Base64.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/Base64.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/Base64.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/Base64.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/Base64.cpp:26: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o In file included from pwiz/utility/misc/BinaryData.cpp:25: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/BinaryData.cpp:25: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/BinaryData.cpp:25: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ pwiz/utility/misc/BinaryData.cpp:303:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma managed(push, off) ^ pwiz/utility/misc/BinaryData.cpp:475:9: warning: unknown pragma ignored [-Wunknown-pragmas] #pragma managed(pop) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o In file included from pwiz/utility/misc/IterationListener.cpp:26: In file included from pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/IterationListener.cpp:26: In file included from pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/IterationListener.cpp:26: In file included from pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/IterationListener.cpp:26: In file included from pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/IterationListener.cpp:26: In file included from pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o In file included from pwiz/utility/misc/MSIHandler.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/MSIHandler.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/MSIHandler.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/MSIHandler.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/MSIHandler.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:31: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:31: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:33: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/Filesystem.cpp:58: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:13: In file included from ./boost/spirit/home/karma/char.hpp:13: In file included from ./boost/spirit/home/karma/char/char.hpp:15: In file included from ./boost/spirit/home/support/string_traits.hpp:16: In file included from ./boost/spirit/home/support/container.hpp:21: In file included from ./boost/variant.hpp:17: In file included from ./boost/variant/variant.hpp:30: In file included from ./boost/variant/detail/initializer.hpp:21: In file included from ./boost/detail/reference_content.hpp:19: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/utility/misc/Filesystem.cpp:26: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here : T::type ^ ./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_>' requested here : T::type ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:25:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T1)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>, mpl_::bool_, mpl_::bool_, mpl_::bool_>' requested here : aux::and_impl< ^ ./boost/mpl/iter_fold_if.hpp:42:11: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) : and_< ^ ./boost/mpl/iter_fold_if.hpp:85:9: note: in instantiation of template class 'boost::mpl::aux::iter_fold_if_impl, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect, boost::mpl::l_iter>>, mpl_::na, boost::mpl::always>>' requested here aux::iter_fold_if_impl< ^ ./boost/mpl/iter_fold_if.hpp:102:20: note: in instantiation of member class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>::result_' requested here typename result_::state ^ ./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>' requested here typedef typename mpl::iter_fold_if< ^ ./boost/variant/variant.hpp:1250:39: note: in instantiation of template class 'boost::detail::variant::find_fallback_type, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>' requested here typedef typename detail::variant::find_fallback_type< ^ ./boost/spirit/home/support/info.hpp:69:20: note: in instantiation of template class 'boost::variant, boost::recursive_wrapper, boost::recursive_wrapper>, boost::recursive_wrapper>>' requested here value_type value; ^ In file included from pwiz/utility/misc/Filesystem.cpp:58: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:21: In file included from ./boost/spirit/home/karma/binary.hpp:13: In file included from ./boost/spirit/home/karma/binary/binary.hpp:15: In file included from ./boost/spirit/home/support/detail/endian.hpp:19: In file included from ./boost/endian/arithmetic.hpp:30: In file included from ./boost/endian/buffers.hpp:30: In file included from ./boost/endian/detail/endian_store.hpp:12: In file included from ./boost/endian/detail/is_trivially_copyable.hpp:11: ./boost/type_traits/has_trivial_assign.hpp:29:7: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value && is_assignable::value) ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o In file included from pwiz/utility/misc/TabReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/TabReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/TabReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/TabReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/TabReader.cpp:25: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field] comment_char = comment_char; ^ 6 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:76: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:76: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:76: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:76: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:76: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o In file included from pwiz/utility/misc/SHA1Calculator.cpp:33: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/SHA1Calculator.cpp:33: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:13: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/SHA1Calculator.cpp:33: In file included from ./pwiz/utility/misc/Std.hpp:29: In file included from ./pwiz/utility/misc/Environment.hpp:24: In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:14: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/SHA1Calculator.cpp:33: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/SHA1Calculator.cpp:33: In file included from ./pwiz/utility/misc/Std.hpp:31: In file included from ./pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o In file included from pwiz/utility/misc/sha1calc.cpp:25: In file included from pwiz/utility/misc/unit.hpp:29: In file included from pwiz/utility/misc/DateTime.hpp:25: In file included from ./boost/date_time/local_time/local_time.hpp:19: In file included from ./boost/date_time/local_time/tz_database.hpp:14: In file included from ./boost/date_time/tz_db_base.hpp:24: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/sha1calc.cpp:25: In file included from pwiz/utility/misc/unit.hpp:29: In file included from pwiz/utility/misc/DateTime.hpp:25: In file included from ./boost/date_time/local_time/local_time.hpp:19: In file included from ./boost/date_time/local_time/tz_database.hpp:14: In file included from ./boost/date_time/tz_db_base.hpp:24: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/sha1calc.cpp:25: In file included from pwiz/utility/misc/unit.hpp:30: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/sha1calc.cpp:25: In file included from pwiz/utility/misc/unit.hpp:30: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/utility/misc/sha1calc.cpp:25: In file included from pwiz/utility/misc/unit.hpp:30: In file included from pwiz/utility/misc/Filesystem.hpp:34: In file included from pwiz/utility/misc/String.hpp:33: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ 5 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:31: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:31: In file included from ./boost/algorithm/string.hpp:23: In file included from ./boost/algorithm/string/split.hpp:16: In file included from ./boost/algorithm/string/iter_find.hpp:27: In file included from ./boost/algorithm/string/find_iterator.hpp:24: In file included from ./boost/algorithm/string/detail/find_iterator.hpp:18: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:33: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant ::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{}; ^ ./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) ^ In file included from pwiz/utility/misc/String.cpp:24: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:13: In file included from ./boost/spirit/home/karma/char.hpp:13: In file included from ./boost/spirit/home/karma/char/char.hpp:15: In file included from ./boost/spirit/home/support/string_traits.hpp:16: In file included from ./boost/spirit/home/support/container.hpp:21: In file included from ./boost/variant.hpp:17: In file included from ./boost/variant/variant.hpp:30: In file included from ./boost/variant/detail/initializer.hpp:21: In file included from ./boost/detail/reference_content.hpp:19: ./boost/type_traits/has_nothrow_copy.hpp:36:89: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_copy_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:202:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value && is_copy_constructible::value) ^ In file included from pwiz/utility/misc/String.cpp:21: In file included from pwiz/utility/misc/String.hpp:32: In file included from ./boost/format.hpp:38: In file included from ./boost/format/internals.hpp:21: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor' requested here : T::type ^ ./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_>' requested here : T::type ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:25:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>>' requested here BOOST_MPL_AUX_NESTED_TYPE_WKND(T1)::value ^ ./boost/mpl/aux_/nested_type_wknd.hpp:38:24: note: expanded from macro 'BOOST_MPL_AUX_NESTED_TYPE_WKND' ::boost::mpl::aux::nested_type_wknd \ ^ ./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl, boost::mpl::l_iter, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>>, mpl_::bool_, mpl_::bool_, mpl_::bool_>' requested here : aux::and_impl< ^ ./boost/mpl/iter_fold_if.hpp:42:11: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) : and_< ^ ./boost/mpl/iter_fold_if.hpp:85:9: note: in instantiation of template class 'boost::mpl::aux::iter_fold_if_impl, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect, boost::mpl::l_iter>>, mpl_::na, boost::mpl::always>>' requested here aux::iter_fold_if_impl< ^ ./boost/mpl/iter_fold_if.hpp:102:20: note: in instantiation of member class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>::result_' requested here typename result_::state ^ ./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect>, boost::mpl::protect>' requested here typedef typename mpl::iter_fold_if< ^ ./boost/variant/variant.hpp:1250:39: note: in instantiation of template class 'boost::detail::variant::find_fallback_type, boost::spirit::info::nil_, boost::mpl::l_item, std::basic_string, boost::mpl::l_item, boost::recursive_wrapper, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_item, boost::recursive_wrapper>, boost::mpl::l_end>>>>>>' requested here typedef typename detail::variant::find_fallback_type< ^ ./boost/spirit/home/support/info.hpp:69:20: note: in instantiation of template class 'boost::variant, boost::recursive_wrapper, boost::recursive_wrapper>, boost::recursive_wrapper>>' requested here value_type value; ^ In file included from pwiz/utility/misc/String.cpp:24: In file included from ./boost/spirit/include/karma.hpp:16: In file included from ./boost/spirit/home/karma.hpp:21: In file included from ./boost/spirit/home/karma/binary.hpp:13: In file included from ./boost/spirit/home/karma/binary/binary.hpp:15: In file included from ./boost/spirit/home/support/detail/endian.hpp:19: In file included from ./boost/endian/arithmetic.hpp:30: In file included from ./boost/endian/buffers.hpp:30: In file included from ./boost/endian/detail/endian_store.hpp:12: In file included from ./boost/endian/detail/is_trivially_copyable.hpp:11: ./boost/type_traits/has_trivial_assign.hpp:29:7: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value && is_assignable::value) ^ 8 warnings generated. clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o clang++ -arch arm64 -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o In file included from boost/libs/thread/src/pthread/thread.cpp:19: In file included from ./boost/thread/future.hpp:51: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:38: ./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] template struct has_nothrow_constructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible::value) ^ In file included from boost/libs/thread/src/pthread/thread.cpp:19: In file included from ./boost/thread/future.hpp:51: In file included from ./boost/optional.hpp:15: In file included from ./boost/optional/optional.hpp:47: In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16: ./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] BOOST_HAS_NOTHROW_ASSIGN(T) ^ ./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value && is_assignable::value) ^ In file included from boost/libs/thread/src/pthread/thread.cpp:19: In file included from ./boost/thread/future.hpp:65: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:22: ./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX ^ ./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value) ^ In file included from boost/libs/thread/src/pthread/thread.cpp:19: In file included from ./boost/thread/future.hpp:65: In file included from ./boost/function.hpp:30: In file included from ./boost/function/detail/prologue.hpp:17: In file included from ./boost/function/function_base.hpp:23: ./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] template struct has_trivial_destructor : public integral_constant{}; ^ ./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible::value) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mzR.so 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/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_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/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.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/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/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/mzR.buildbin-libdir/00LOCK-mzR/00new/mzR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mzR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mzR.buildbin-libdir/mzR/libs/mzR.so >>>>>>> >>>>>>> Paths before fix: mzR.buildbin-libdir/mzR/libs/mzR.so: mzR.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "mzR.buildbin-libdir/mzR/libs/mzR.so" >>>>>>> Paths after fix: mzR.buildbin-libdir/mzR/libs/mzR.so: mzR.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)