##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mzR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mzR_2.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mzR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  RcppPwiz.cpp:408:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  RcppPwiz.cpp:778:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  RcppPwiz.cpp:854:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr<pwiz::chemistry::Formula>' is deprecated [-Wdeprecated-declarations]
  pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/mzR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/mzR/libs/mzR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/mzR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mzR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<pwiz::data::MemoryIndex::Impl>' 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<pwiz::data::MemoryIndex::Impl>' 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<pwiz::data::MemoryIndex::Impl, pwiz::data::MemoryIndex::Impl>' requested here
        boost::detail::sp_pointer_construct( this, p, pn );
                       ^
pwiz/data/common/MemoryIndex.cpp:73:44: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::MemoryIndex::Impl>::shared_ptr<pwiz::data::MemoryIndex::Impl>' requested here
PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
                                           ^
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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl, pwiz::data::BinaryIndexStream::Impl>' 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<pwiz::data::BinaryIndexStream::Impl>::shared_ptr<pwiz::data::BinaryIndexStream::Impl>' requested here
PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
                                                                                 ^
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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <bool, ((::boost::is_pod<T>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<const char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' 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::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
            return ::boost::algorithm::iter_split(
                                       ^
pwiz/data/common/Unimod.cpp:131:22: note: in instantiation of function template specialization 'boost::algorithm::split<std::vector<std::basic_string<char>>, const std::basic_string<char> &, 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<const char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' 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::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
            return ::boost::algorithm::iter_split(
                                       ^
pwiz/data/common/Unimod.cpp:131:22: note: in instantiation of function template specialization 'boost::algorithm::split<std::vector<std::basic_string<char>>, const std::basic_string<char> &, 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor<boost::spirit::info::nil_>' requested here
    : T::type
      ^
./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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<T> \
                       ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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<T> \
                       ^
./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl<true, boost::mpl::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>>, mpl_::bool_<true>, mpl_::bool_<true>, mpl_::bool_<true>>' 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::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::mpl::aux::iter_fold_if_pred<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<l_end>>>, mpl_::na, boost::mpl::always<mpl_::bool_<false>>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>::result_' requested here
          typename result_::state
                   ^
./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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::spirit::info::nil_, std::basic_string<char>, boost::recursive_wrapper<boost::spirit::info>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::recursive_wrapper<std::list<boost::spirit::info>>>' 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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>>' requested here
template <class T> struct has_trivial_default_constructor : public has_trivial_constructor<T> {};
                                                                   ^
./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>>' 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_<boost::has_trivial_default_constructor<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>>, boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>, boost::range_detail::default_constructible_unary_fn_wrapper<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>, const std::basic_string<char> &>>' 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<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>, const std::basic_string<char> &>' 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<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>, std::__map_const_iterator<std::__tree_const_iterator<std::__value_type<std::basic_string<char>, std::basic_string<char>>, std::__tree_node<std::__value_type<std::basic_string<char>, std::basic_string<char>>, 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<boost::range_detail::select_first<std::map<std::basic_string<char>, std::basic_string<char>>>, const std::map<std::basic_string<char>, std::basic_string<char>>>' 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::map<std::basic_string<char>, std::basic_string<char>>>' 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <boost/bind/bind.hpp> + 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)))
                                 ^
<scratch space>:290:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<const char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            return ::boost::algorithm::iter_split(
                                       ^
pwiz/data/msdata/MSData.cpp:508:12: note: in instantiation of function template specialization 'boost::algorithm::split<std::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<const char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            return ::boost::algorithm::iter_split(
                                       ^
pwiz/data/msdata/MSData.cpp:508:12: note: in instantiation of function template specialization 'boost::algorithm::split<std::vector<std::basic_string<char>>, const std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::value)
                                        ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_copy_constructor<unsigned int>' 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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/type_traits/has_nothrow_constructor.hpp:69:68: note: in instantiation of template class 'boost::has_nothrow_constructor<unsigned int>' requested here
template <class T> struct has_nothrow_default_constructor : public has_nothrow_constructor<T>{};
                                                                   ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_default_constructor<unsigned int>' 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<T>::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<T>::value && is_assignable<T&, const T&>::value)
                                          ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_assign<unsigned int>' 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<T>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::value)
                                        ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_copy_constructor<unsigned int>' 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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/type_traits/has_nothrow_constructor.hpp:69:68: note: in instantiation of template class 'boost::has_nothrow_constructor<unsigned int>' requested here
template <class T> struct has_nothrow_default_constructor : public has_nothrow_constructor<T>{};
                                                                   ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_default_constructor<unsigned int>' 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<T>::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<T>::value && is_assignable<T&, const T&>::value)
                                          ^
./boost/serialization/serialization.hpp:52:1: note: in instantiation of template class 'boost::has_nothrow_assign<unsigned int>' 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<T>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<pwiz::identdata::(anonymous namespace)::EnzymePtr_name>' requested here
template <class T> struct has_trivial_default_constructor : public has_trivial_constructor<T> {};
                                                                   ^
./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_name>' 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_<boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_name>, pwiz::identdata::(anonymous namespace)::EnzymePtr_name, boost::range_detail::default_constructible_unary_fn_wrapper<pwiz::identdata::(anonymous namespace)::EnzymePtr_name, std::basic_string<char>>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_name, std::basic_string<char>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_name, std::__wrap_iter<const boost::shared_ptr<pwiz::identdata::Enzyme> *>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_name, const std::vector<boost::shared_ptr<pwiz::identdata::Enzyme>>>' 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 <bool, ((::boost::is_pod<T>::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<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity>' requested here
template <class T> struct has_trivial_default_constructor : public has_trivial_constructor<T> {};
                                                                   ^
./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity>' 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_<boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity>, pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, boost::range_detail::default_constructible_unary_fn_wrapper<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, int>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, int>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, std::__wrap_iter<const boost::shared_ptr<pwiz::identdata::Enzyme> *>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_specificity, const std::vector<boost::shared_ptr<pwiz::identdata::Enzyme>>>' 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 <bool, ((::boost::is_pod<T>::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<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages>' requested here
template <class T> struct has_trivial_default_constructor : public has_trivial_constructor<T> {};
                                                                   ^
./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages>' 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_<boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages>, pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, boost::range_detail::default_constructible_unary_fn_wrapper<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, int>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, int>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, std::__wrap_iter<const boost::shared_ptr<pwiz::identdata::Enzyme> *>>' 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<pwiz::identdata::(anonymous namespace)::EnzymePtr_missedCleavages, const std::vector<boost::shared_ptr<pwiz::identdata::Enzyme>>>' 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 <bool, ((::boost::is_pod<T>::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<pwiz::identdata::(anonymous namespace)::CVParam_name>' requested here
template <class T> struct has_trivial_default_constructor : public has_trivial_constructor<T> {};
                                                                   ^
./boost/mpl/if.hpp:63:68: note: in instantiation of template class 'boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::CVParam_name>' 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_<boost::has_trivial_default_constructor<pwiz::identdata::(anonymous namespace)::CVParam_name>, pwiz::identdata::(anonymous namespace)::CVParam_name, boost::range_detail::default_constructible_unary_fn_wrapper<pwiz::identdata::(anonymous namespace)::CVParam_name, std::basic_string<char>>>' 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<pwiz::identdata::(anonymous namespace)::CVParam_name, std::basic_string<char>>' 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<pwiz::identdata::(anonymous namespace)::CVParam_name, std::__wrap_iter<pwiz::data::CVParam *>>' 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<pwiz::identdata::(anonymous namespace)::CVParam_name, std::vector<pwiz::data::CVParam>>' 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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<const char *>, const char *, const char *>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<const char *>, const char *, const char *>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<const char *>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<const char *>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, const char *const &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::vector<std::basic_string<char>>, const char *const &, boost::algorithm::detail::is_any_ofF<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<const char *>, const char *, const char *>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<const char *>, const char *, const char *>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<const char *>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<const char *>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, const char *const &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::vector<std::basic_string<char>>, const char *const &, boost::algorithm::detail::is_any_ofF<char>>' 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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::value)
                                          ^
pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
            BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(c.get())->affiliations)
            ^
./boost/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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/identdata/MascotReader.cpp:26:
pwiz/data/identdata/MascotReader.hpp:62:11: warning: private field 'pimpl' is not used [-Wunused-private-field]
    Impl* pimpl;
          ^
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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::value)
                                          ^
pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr<pwiz::chemistry::Formula>' is deprecated [-Wdeprecated-declarations]
    auto_ptr<Formula> formula_;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<pwiz::chemistry::Formula>' 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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:104:21: note: in instantiation of function template specialization 'boost::algorithm::find_iterator<std::__wrap_iter<const char *>>::find_iterator<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::vector<boost::iterator_range<std::__wrap_iter<const char *>>>, const std::basic_string<char> &, boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::vector<boost::iterator_range<std::__wrap_iter<const char *>>>, const std::basic_string<char> &, std::basic_string<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::assign_to<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<boost::iterator_range<std::__wrap_iter<const char *>>, std::__wrap_iter<const char *>, std::__wrap_iter<const char *>>::function2<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::__wrap_iter<const char *>>::find_iterator_base<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:104:21: note: in instantiation of function template specialization 'boost::algorithm::find_iterator<std::__wrap_iter<const char *>>::find_iterator<boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::vector<boost::iterator_range<std::__wrap_iter<const char *>>>, const std::basic_string<char> &, boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, 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<std::vector<boost::iterator_range<std::__wrap_iter<const char *>>>, const std::basic_string<char> &, std::basic_string<char>>' 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<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, ModificationList, key_compare, allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::value)
                                        ^
./boost/type_traits/has_trivial_copy.hpp:57:65: note: in instantiation of template class 'boost::has_trivial_copy<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
template <class T> struct has_trivial_copy_constructor : public has_trivial_copy<T>{};
                                                                ^
./boost/function/function_template.hpp:945:20: note: in instantiation of template class 'boost::has_trivial_copy_constructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
        if (boost::has_trivial_copy_constructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::value)
                                              ^
./boost/function/function_template.hpp:946:20: note: in instantiation of template class 'boost::has_trivial_destructor<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
            boost::has_trivial_destructor<Functor>::value &&
                   ^
./boost/function/function_template.hpp:720:13: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::assign_to<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
      this->assign_to(f);
            ^
./boost/algorithm/string/detail/find_iterator.hpp:51:21: note: in instantiation of function template specialization 'boost::function2<boost::iterator_range<std::__wrap_iter<char *>>, std::__wrap_iter<char *>, std::__wrap_iter<char *>>::function2<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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<std::__wrap_iter<char *>>::find_iterator_base<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
                detail::find_iterator_base<IteratorT>(Finder,0),
                ^
./boost/algorithm/string/iter_find.hpp:178:21: note: in instantiation of function template specialization 'boost::algorithm::split_iterator<std::__wrap_iter<char *>>::split_iterator<boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' 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::vector<std::basic_string<char>>, std::basic_string<char> &, boost::algorithm::detail::is_any_ofF<char>>' 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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor<boost::spirit::info::nil_>' requested here
    : T::type
      ^
./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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<T> \
                       ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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<T> \
                       ^
./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl<true, boost::mpl::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>>, mpl_::bool_<true>, mpl_::bool_<true>, mpl_::bool_<true>>' 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::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::mpl::aux::iter_fold_if_pred<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<l_end>>>, mpl_::na, boost::mpl::always<mpl_::bool_<false>>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>::result_' requested here
          typename result_::state
                   ^
./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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::spirit::info::nil_, std::basic_string<char>, boost::recursive_wrapper<boost::spirit::info>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::recursive_wrapper<std::list<boost::spirit::info>>>' 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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor<boost::spirit::info::nil_>' requested here
    : T::type
      ^
./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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<T> \
                       ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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<T> \
                       ^
./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl<true, boost::mpl::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>>, mpl_::bool_<true>, mpl_::bool_<true>, mpl_::bool_<true>>' 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::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::mpl::aux::iter_fold_if_pred<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<l_end>>>, mpl_::na, boost::mpl::always<mpl_::bool_<false>>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>::result_' requested here
          typename result_::state
                   ^
./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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::spirit::info::nil_, std::basic_string<char>, boost::recursive_wrapper<boost::spirit::info>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::recursive_wrapper<std::list<boost::spirit::info>>>' 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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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 <bool, ((::boost::is_pod<T>::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 <class T> struct has_nothrow_copy_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_COPY(T)>{};
                                                                                        ^
./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<T>::value && !is_reference<T>::value && is_copy_constructible<T>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::value)
                                               ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::has_nothrow_constructor<boost::spirit::info::nil_>' requested here
    : T::type
      ^
./boost/mpl/not.hpp:41:11: note: in instantiation of template class 'boost::mpl::aux::nested_type_wknd<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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<T> \
                       ^
./boost/mpl/aux_/nested_type_wknd.hpp:27:7: note: in instantiation of template class 'boost::mpl::not_<boost::has_nothrow_constructor<boost::spirit::info::nil_>>' 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::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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<T> \
                       ^
./boost/mpl/aux_/preprocessed/gcc/and.hpp:50:7: note: in instantiation of template class 'boost::mpl::aux::and_impl<true, boost::mpl::apply1<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>>, mpl_::bool_<true>, mpl_::bool_<true>, mpl_::bool_<true>>' 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::mpl::l_iter<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::mpl::aux::iter_fold_if_pred<boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>, boost::mpl::l_iter<l_end>>>, mpl_::na, boost::mpl::always<mpl_::bool_<false>>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>::result_' requested here
          typename result_::state
                   ^
./boost/variant/variant.hpp:190:27: note: in instantiation of template class 'boost::mpl::iter_fold_if<boost::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, boost::mpl::l_end>>>>>, mpl_::int_<0>, boost::mpl::protect<boost::mpl::next<na>>, boost::mpl::protect<boost::detail::variant::find_fallback_type_pred>>' 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::mpl::l_item<mpl_::long_<5>, boost::spirit::info::nil_, boost::mpl::l_item<mpl_::long_<4>, std::basic_string<char>, boost::mpl::l_item<mpl_::long_<3>, boost::recursive_wrapper<boost::spirit::info>, boost::mpl::l_item<mpl_::long_<2>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::mpl::l_item<mpl_::long_<1>, boost::recursive_wrapper<std::list<boost::spirit::info>>, 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::spirit::info::nil_, std::basic_string<char>, boost::recursive_wrapper<boost::spirit::info>, boost::recursive_wrapper<std::pair<boost::spirit::info, boost::spirit::info>>, boost::recursive_wrapper<std::list<boost::spirit::info>>>' 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<T>::value && is_assignable<T&, const T&>::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 <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./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<T>::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<T>::value && is_assignable<T&, const T&>::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<T>::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 <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./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<T>::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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library("mzR")
Loading required package: Rcpp
> library("msdata")
> 
> 
> ## Catch warnings as well:
> #options(warn = 2)
> 
> BiocGenerics:::testPackage("mzR")
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Unknown IO errorfailed to load external entity "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd"
Element '{http://www.w3.org/2001/XMLSchema}include': Failed to load the document 'http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd' for inclusion.


RUNIT TEST PROTOCOL -- Mon Jun 10 23:34:41 2024 
*********************************************** 
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
3: In XML::xmlTreeParse(system.file("extdata", "mzXML_idx_3.2.xsd.xml",  :
  NULL value for external reference
> 
> proc.time()
   user  system elapsed 
 32.734   2.323  50.481