Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1388/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mzR 2.40.0 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the mzR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mzR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: mzR |
Version: 2.40.0 |
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_2.40.0.tar.gz |
StartedAt: 2024-12-21 03:00:37 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 03:02:33 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 116.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mzR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mzR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mzR’ version ‘2.40.0’ * 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-3.20-bioc/meat/mzR.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 11.2Mb sub-directories of 1Mb or more: libs 10.6Mb * 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-3.20-bioc/meat/mzR.Rcheck/00check.log’ for details.
mzR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o In file included from RcppPwiz.cpp:1: In file included from ./RcppPwiz.h:12: In file included from ./pwiz/data/msdata/MSDataFile.hpp:29: In file included from ./pwiz/data/msdata/MSData.hpp:30: In file included from ./pwiz/data/common/ParamTypes.hpp:29: In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36: In file included from ./pwiz/utility/misc/Singleton.hpp:26: In file included from ./boost_aux/boost/utility/singleton.hpp:18: In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32: In file included from ./boost/function_types/function_arity.hpp:12: In file included from ./boost/blank.hpp:26: In file included from ./boost/type_traits/is_stateless.hpp:12: ./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] : public integral_constant <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)
mzR.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 -- Sat Dec 21 03:02:24 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 51.744 2.463 54.201
mzR.Rcheck/mzR-Ex.timings
name | user | system | elapsed | |
copyWriteMSData | 0.146 | 0.015 | 0.158 | |
isolationWindow-methods | 1.679 | 0.115 | 1.793 | |
metadata | 0.184 | 0.022 | 0.210 | |
mzR-class | 0.067 | 0.014 | 0.098 | |
openMSfile | 0.092 | 0.010 | 0.102 | |
peaks | 1.565 | 0.058 | 1.620 | |
writeMSData | 0.105 | 0.014 | 0.116 | |