Steffen Neumann
| Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/mzR |
| git_branch: devel |
| git_last_commit: f768fca |
| git_last_commit_date: 2026-03-22 12:42:54 -0400 (Sun, 22 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-13 11:36 -0400 (Mon, 13 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4632 |
| 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 1456/2390 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mzR 2.45.1 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for mzR in R Universe. | ||||||||||||||
|
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: 2.45.1 |
| 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_2.45.1.tar.gz |
| StartedAt: 2026-04-12 21:02:59 -0400 (Sun, 12 Apr 2026) |
| EndedAt: 2026-04-12 21:08:02 -0400 (Sun, 12 Apr 2026) |
| EllapsedTime: 303.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzR.Rcheck |
| Warnings: 2 |
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### 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_2.45.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/mzR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-13 01:03:00 UTC
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.45.1’
* 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:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
RcppPwiz.cpp:420:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
RcppPwiz.cpp:794:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
RcppPwiz.cpp:891:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
boost/libs/regex/src/posix_api.cpp:182:27: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
boost/libs/regex/src/posix_api.cpp:194:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:51:20: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
pwiz/data/msdata/Serializer_MSn.cpp:80:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
pwiz/data/msdata/Serializer_MSn.cpp:81:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
pwiz/data/msdata/Serializer_MSn.cpp:82:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
pwiz/data/msdata/Serializer_MSn.cpp:83:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, long long>' is deprecated [-Wdeprecated-declarations]
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const double>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const double>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const float>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, float>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const long long>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, long long>' is deprecated [-Wdeprecated-declarations]
pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
Found the following additional notes/warnings:
SystemRequirements specified C++11: support has been removed
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/mzR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... NOTE
Obsolete C++11 standard request will be ignored
* checking installed package size ... INFO
installed size is 18.9Mb
sub-directories of 1Mb or more:
libs 18.3Mb
* 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 ... INFO
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/4.6/Resources/library/mzR/libs/mzR.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Found ‘___assert_rtn’, possibly from ‘assert’ (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 ‘_printf’, possibly from ‘printf’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
peaks 7.666 0.310 8.972
copyWriteMSData 4.801 0.445 5.707
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/mzR.Rcheck/00check.log’
for details.
mzR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mzR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘mzR’ ...
** this is package ‘mzR’ version ‘2.45.1’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
RcppPwiz.cpp:420:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
420 | Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);
| ~~ ^~~~~~~
| %zu
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:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
RcppPwiz.cpp:437:42: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
437 | data.insert(data.end(), ints->data.begin(), ints->data.end());
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
RcppPwiz.cpp:794:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
794 | if ( (precursorScanNum[i] > 0) | (precursorMZ[i] > 0) ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| ||
RcppPwiz.cpp:794:10: note: cast one or both operands to int to silence this warning
RcppPwiz.cpp:891:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
891 | Rprintf("Index whichChrom out of bounds [1 ... %d].\n", (clp->size()));
| ~~ ^~~~~~~~~~~~~
| %zu
13 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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
boost/libs/regex/src/posix_api.cpp:182:27: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
182 | int r = (std::sprintf)(localbuf, "%d", i);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
boost/libs/regex/src/posix_api.cpp:194:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
194 | int r = (std::sprintf)(localbuf, "%d", 0);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | 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
154 | 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
279 | 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
373 | 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
73 | PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
145 | 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
145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
| ^
| ( )
pwiz/data/common/CVTranslator.cpp:146:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
| ~~
146 | 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
146 | 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]
146 | key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
| ~~
147 | 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
147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
| ^
| ( )
pwiz/data/common/CVTranslator.cpp:148:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
| ~~
148 | 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
148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
| ^
| ( )
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
pwiz/data/common/ParamTypes.cpp:212:37: warning: unused variable 'it' [-Wunused-variable]
212 | vector<CVParam>::const_iterator it;
| ^~
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | 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
154 | 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
279 | 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
373 | 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
417 | PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible<T>::value)
| ^
In file included from pwiz/data/common/Unimod.cpp:25:
pwiz/data/common/Unimod.hpp:69:1: warning: all paths through this function will call itself [-Winfinite-recursion]
69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
| ^
./boost_aux/boost/enum/macros.hpp:234:5: note: expanded from macro 'BOOST_BITFIELD_DOMAIN_OPERATORS'
234 | BOOST_ENUM_DOMAIN_OPERATORS(_name) \
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
In file included from pwiz/data/common/Unimod.cpp:25:
pwiz/data/common/Unimod.hpp:78:1: warning: all paths through this function will call itself [-Winfinite-recursion]
78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
In file included from pwiz/data/common/Unimod.cpp:25:
pwiz/data/common/Unimod.hpp:97:1: warning: all paths through this function will call itself [-Winfinite-recursion]
97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
| ^
./boost_aux/boost/enum/macros.hpp:234:5: note: expanded from macro 'BOOST_BITFIELD_DOMAIN_OPERATORS'
234 | BOOST_ENUM_DOMAIN_OPERATORS(_name) \
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
158 | 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::string>, const std::string &, boost::algorithm::detail::is_classifiedF>' requested here
131 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_classifiedF>>' requested here
158 | 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::string>, const std::string &, boost::algorithm::detail::is_classifiedF>' requested here
131 | bal::split(formulaTokens, itr->second, bal::is_space());
| ^
13 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:51:20: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
51 | size_t n = sprintf(id, "%s:%07lu", cvrefs_[index].prefix,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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:80:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
80 | sprintf(header.header[0], "CreationDate %s", ctime(&rawtime));
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
pwiz/data/msdata/Serializer_MSn.cpp:81:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
81 | sprintf(header.header[1], "Extractor\tProteoWizard\n");
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
pwiz/data/msdata/Serializer_MSn.cpp:82:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
82 | sprintf(header.header[2], "Extractor version\t%s\n", (msd.softwarePtrs.empty() ? "unknown" : msd.softwarePtrs.at(0)->id.c_str()));
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
pwiz/data/msdata/Serializer_MSn.cpp:83:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
83 | sprintf(header.header[3], "Source file\t%s\n", (msd.fileDescription.sourceFilePtrs.empty() ? "unknown" : msd.fileDescription.sourceFilePtrs.at(0)->name.c_str()));
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
pwiz/data/msdata/Serializer_MSn.cpp:44:11: warning: unused variable 'sizeChargeMSn' [-Wunused-const-variable]
44 | 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]
45 | const int sizePeakMSn = 12; // struct Peak{ double mz; float intensity; }
| ^~~~~~~~~~~
14 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible<T>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | 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'
202 | # 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]
27 | 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'
199 | # 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
27 | : 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
41 | 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'
38 | ::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
27 | : 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::string, 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
25 | 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'
38 | ::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::string, 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
50 | : 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)
42 | : 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::string, 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
85 | 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::string, 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
102 | 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::string, 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
190 | 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::string, 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
1250 | 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::string, 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
69 | 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]
29 | BOOST_HAS_TRIVIAL_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN'
193 | # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
41 | : 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'
187 | # 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::string, std::string>>>' requested here
51 | 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::string, std::string>>>' requested here
63 | 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::string, std::string>>>, boost::range_detail::select_first<std::map<std::string, std::string>>, boost::range_detail::default_constructible_unary_fn_wrapper<boost::range_detail::select_first<std::map<std::string, std::string>>, const std::string &>>' requested here
71 | 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::string, std::string>>, const std::string &>' requested here
31 | 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::string, std::string>>, std::__map_const_iterator<std::__tree_const_iterator<std::__value_type<std::string, std::string>, std::__tree_node<std::__value_type<std::string, std::string>, void *> *, long>>>' requested here
42 | 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::string, std::string>>, const std::map<std::string, std::string>>' requested here
65 | : 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::string, std::string>>' requested here
62 | auto actualIdKeys = actualId | boost::adaptors::map_keys;
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
243 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
243 | 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:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
./pwiz/utility/misc/BinaryData.hpp:247:20: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
247 | return *(--end());
| ^
./pwiz/utility/misc/BinaryData.hpp:365:9: note: in instantiation of member function 'pwiz::util::BinaryData<double>::back' requested here
365 | back() = value;
| ^
pwiz/data/msdata/SpectrumList_MGF.cpp:315:33: note: in instantiation of member function 'pwiz::util::BinaryData<double>::push_back' requested here
315 | mzArray.push_back(mz);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | BOOST_PRAGMA_MESSAGE(
| ^
./boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^
<scratch space>:51:2: note: expanded from here
51 | 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.")
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
641 | size_t lineCount = 0;
| ^
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:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
./pwiz/utility/misc/BinaryData.hpp:247:20: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
247 | return *(--end());
| ^
./pwiz/utility/misc/BinaryData.hpp:365:9: note: in instantiation of member function 'pwiz::util::BinaryData<double>::back' requested here
365 | back() = value;
| ^
pwiz/data/msdata/SpectrumList_MSn.cpp:404:25: note: in instantiation of member function 'pwiz::util::BinaryData<double>::push_back' requested here
404 | mzArray.push_back(mz);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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/BinaryDataEncoder.cpp:26:
In file included from pwiz/data/msdata/BinaryDataEncoder.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/data/msdata/BinaryDataEncoder.cpp:459:54: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
459 | copy(floatBuffer, floatBuffer+floatCount, result.begin());
| ^
pwiz/data/msdata/BinaryDataEncoder.cpp:571:17: note: in instantiation of function template specialization 'pwiz::msdata::copyBuffer<double, float>' requested here
571 | copyBuffer<T, T32>(byteBuffer, byteCount, result);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
In file included from pwiz/data/msdata/BinaryDataEncoder.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, long long>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/data/msdata/BinaryDataEncoder.cpp:459:54: note: in instantiation of member class 'pwiz::util::BinaryData<long long>::iterator' requested here
459 | copy(floatBuffer, floatBuffer+floatCount, result.begin());
| ^
pwiz/data/msdata/BinaryDataEncoder.cpp:651:9: note: in instantiation of function template specialization 'pwiz::msdata::copyBuffer<long long, int>' requested here
651 | copyBuffer<T, T32>(byteBuffer, byteCount, result);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, long long>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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/MSData.cpp:25:
In file included from pwiz/data/msdata/MSData.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/data/msdata/MSData.cpp:893:36: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
893 | bd_mz->data.insert(bd_mz->data.end(), mzArray.begin(), mzArray.end());
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/data/msdata/MSData.cpp:25:
In file included from pwiz/data/msdata/MSData.hpp:29:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const double>' is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
| ^
pwiz/data/msdata/MSData.cpp:893:51: note: in instantiation of member class 'pwiz::util::BinaryData<double>::const_iterator' requested here
893 | bd_mz->data.insert(bd_mz->data.end(), mzArray.begin(), mzArray.end());
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, const double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, const std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
508 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, const std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
508 | boost::split(pairs, id, boost::is_any_of(" \t\n\r"));
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
163 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
163 | boost::algorithm::split(strCharges, possibleCharges, boost::is_any_of(","));
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
2132 | 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
2132 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
| ^
| ( )
pwiz/data/msdata/IO.cpp:2836:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
2836 | 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
2836 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
| ^
| ( )
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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_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:29:
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
./pwiz/utility/misc/BinaryData.hpp:247:20: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
247 | return *(--end());
| ^
./pwiz/utility/misc/BinaryData.hpp:365:9: note: in instantiation of member function 'pwiz::util::BinaryData<double>::back' requested here
365 | back() = value;
| ^
pwiz/data/msdata/SpectrumList_BTDX.cpp:138:26: note: in instantiation of member function 'pwiz::util::BinaryData<double>::push_back' requested here
138 | mzArray_.push_back(mzValue);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
pwiz/data/msdata/SpectrumList_BTDX.cpp:279:19: warning: private field 'msd_' is not used [-Wunused-private-field]
279 | const MSData& msd_;
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
29 | BOOST_HAS_TRIVIAL_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN'
193 | # 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]
27 | 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'
199 | # 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]
36 | 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'
202 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
125 | return (done() && &that.spectrumList_==&pastEndMarker_ ||
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
pwiz/data/msdata/SpectrumIterator.cpp:125:20: note: place parentheses around the '&&' expression to silence this warning
125 | return (done() && &that.spectrumList_==&pastEndMarker_ ||
| ^
| ( )
pwiz/data/msdata/SpectrumIterator.cpp:126:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
125 | return (done() && &that.spectrumList_==&pastEndMarker_ ||
| ~~
126 | &spectrumList_==&pastEndMarker_ && that.done() ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:126:45: note: place parentheses around the '&&' expression to silence this warning
126 | &spectrumList_==&pastEndMarker_ && that.done() ||
| ^
| ( )
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
126 | &spectrumList_==&pastEndMarker_ && that.done() ||
| ~~
127 | &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: note: place parentheses around the '&&' expression to silence this warning
127 | &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
| ^
| ( )
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: '&&' within '||' [-Wlogical-op-parentheses]
141 | return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
pwiz/data/msdata/SpectrumIterator.cpp:141:34: note: place parentheses around the '&&' expression to silence this warning
141 | return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
| ^
| ( )
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
39 | return !mobilityBounds ||
| ~~
40 | 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
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ^
| ( )
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
27 | 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'
199 | # 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]
36 | 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'
202 | # 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'
202 | # 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:39:54: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
39 | 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]
27 | 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'
199 | # 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
69 | 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:40:34: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
40 | 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:42:57: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
42 | D& operator=(const D& rhs) BOOST_NOEXCEPT_IF(boost::has_nothrow_assign<T>::value) {t = rhs.t; return *this;} \
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | 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'
202 | # 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'
202 | # 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:39:54: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
39 | 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]
27 | 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'
199 | # 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
69 | 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:40:34: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
40 | 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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
52 | BOOST_STRONG_TYPEDEF(unsigned int, version_type)
| ^
./boost/serialization/strong_typedef.hpp:42:57: note: expanded from macro 'BOOST_STRONG_TYPEDEF'
42 | D& operator=(const D& rhs) BOOST_NOEXCEPT_IF(boost::has_nothrow_assign<T>::value) {t = rhs.t; return *this;} \
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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:30:
./pwiz/data/common/Unimod.hpp:69:1: warning: all paths through this function will call itself [-Winfinite-recursion]
69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
| ^
./boost_aux/boost/enum/macros.hpp:234:5: note: expanded from macro 'BOOST_BITFIELD_DOMAIN_OPERATORS'
234 | BOOST_ENUM_DOMAIN_OPERATORS(_name) \
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
In file included from pwiz/data/identdata/IdentData.cpp:30:
./pwiz/data/common/Unimod.hpp:78:1: warning: all paths through this function will call itself [-Winfinite-recursion]
78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
In file included from pwiz/data/identdata/IdentData.cpp:30:
./pwiz/data/common/Unimod.hpp:97:1: warning: all paths through this function will call itself [-Winfinite-recursion]
97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
| ^
./boost_aux/boost/enum/macros.hpp:234:5: note: expanded from macro 'BOOST_BITFIELD_DOMAIN_OPERATORS'
234 | BOOST_ENUM_DOMAIN_OPERATORS(_name) \
| ^
./boost_aux/boost/enum/macros.hpp:226:73: note: expanded from macro 'BOOST_ENUM_DOMAIN_OPERATORS'
226 | inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
| ^
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]
189 | 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 &')
218 | virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
189 | 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 &')
218 | virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
96 | ilr(iterationListenerRegistry),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| nPeptides(0)
97 | strict(strict),
| ^~~~~~~~~~~~~~
| SourceFilesPtr(returnValueSourceFiles)
98 | nPeptides(0),
| ~~~~~~~~~~~~
| ilr(iterationListenerRegistry)
99 | SourceFilesPtr(returnValueSourceFiles)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| strict(strict)
pwiz/data/identdata/Serializer_protXML.cpp:476:10: warning: private field 'readSpectrumQueries' is not used [-Wunused-private-field]
476 | bool readSpectrumQueries;
| ^
pwiz/data/identdata/Serializer_protXML.cpp:477:38: warning: private field 'ilr' is not used [-Wunused-private-field]
477 | const IterationListenerRegistry* ilr;
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
41 | : 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'
187 | # 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
51 | 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
63 | 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::string>>' requested here
71 | 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::string>' requested here
31 | 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
42 | 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
415 | 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]
41 | : 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'
187 | # 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
51 | 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
63 | 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
71 | 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
31 | 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
42 | 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
418 | 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]
41 | : 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'
187 | # 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
51 | 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
63 | 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
71 | 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
31 | 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
42 | 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
504 | 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]
561 | 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
561 | 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]
41 | : 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'
187 | # 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
51 | 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
63 | 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::string>>' requested here
71 | 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::string>' requested here
31 | 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
42 | 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
586 | 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]
1546 | }
| ^
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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const char *const &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, const char *const &, boost::algorithm::detail::is_any_ofF<char>>' requested here
113 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, const char *const &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, const char *const &, boost::algorithm::detail::is_any_ofF<char>>' requested here
113 | 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]
995 | const CVTranslator& _cvTranslator;
| ^
pwiz/data/identdata/Serializer_pepXML.cpp:1450:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
1450 | const CVTranslator& _cvTranslator;
| ^
pwiz/data/identdata/Serializer_pepXML.cpp:1796:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
1796 | const CVTranslator& _cvTranslator;
| ^
pwiz/data/identdata/Serializer_pepXML.cpp:1970:38: warning: private field 'ilr' is not used [-Wunused-private-field]
1970 | const IterationListenerRegistry* ilr;
| ^
21 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
149 | BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(c.get())->affiliations)
| ^
./boost/foreach.hpp:1107:108: note: expanded from macro 'BOOST_FOREACH'
1107 | if (boost::foreach_detail_::auto_any_t BOOST_FOREACH_ID(_foreach_col) = BOOST_FOREACH_CONTAIN(COL)) {} else \
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
189 | 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 &')
218 | 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]
62 | Impl* pimpl;
| ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
98 | 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
104 | 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::string &, boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
71 | 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::string &, std::string>' requested here
468 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
98 | 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
104 | 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::string &, boost::algorithm::detail::first_finderF<std::__wrap_iter<const char *>, boost::algorithm::is_equal>>' requested here
71 | 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::string &, std::string>' requested here
468 | bal::find_all(instances, sequence_, peptide.sequence());
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
189 | 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 &')
218 | 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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
57 | 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
945 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
337 | 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]
30 | 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'
196 | # 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
946 | 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
720 | 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
51 | 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
261 | 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
178 | 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::string>, std::string &, boost::algorithm::detail::token_finderF<boost::algorithm::detail::is_any_ofF<char>>>' requested here
158 | 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::string>, std::string &, boost::algorithm::detail::is_any_ofF<char>>' requested here
337 | split(tokens, massStr, bal::is_any_of(","));
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
36 | 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'
202 | # 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]
27 | 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'
199 | # 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
27 | : 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
41 | 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'
38 | ::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
27 | : 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::string, 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
25 | 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'
38 | ::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::string, 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
50 | : 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)
42 | : 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::string, 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
85 | 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::string, 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
102 | 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::string, 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
190 | 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::string, 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
1250 | 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::string, 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
69 | 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]
29 | BOOST_HAS_TRIVIAL_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN'
193 | # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
pwiz/utility/minimxml/SAXParser.cpp:38:14: warning: unused variable 'comment_begin' [-Wunused-const-variable]
38 | const string comment_begin("!--"), comment_end("--");
| ^~~~~~~~~~~~~
pwiz/utility/minimxml/SAXParser.cpp:38:36: warning: unused variable 'comment_end' [-Wunused-const-variable]
38 | const string comment_begin("!--"), comment_end("--");
| ^~~~~~~~~~~
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
307 | 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
307 | 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]
307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
| ~~
308 | it_==end_ && that.it_==nothing_.end());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/IntegerSet.cpp:308:23: note: place parentheses around the '&&' expression to silence this warning
308 | it_==end_ && that.it_==nothing_.end());
| ^
| ( )
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:25:
In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:25:
In file included from pwiz/utility/misc/optimized_lexical_cast.hpp:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
303 | #pragma managed(push, off)
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const double>' is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
| ^
pwiz/utility/misc/BinaryData.cpp:471:30: note: in instantiation of member class 'pwiz::util::BinaryData<double>::const_iterator' requested here
471 | PWIZ_API_DECL template class BinaryData<double>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, const double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/utility/misc/BinaryData.cpp:299:14: note: in instantiation of member class 'pwiz::util::BinaryData<double>::iterator' requested here
299 | iterator begin_, end_;
| ^
pwiz/utility/misc/BinaryData.cpp:463:21: note: in instantiation of member class 'pwiz::util::BinaryData<double>::Impl' requested here
463 | binaryData._impl->makeIterator(*this, begin);
| ^
pwiz/utility/misc/BinaryData.cpp:471:30: note: in instantiation of member function 'pwiz::util::BinaryData<double>::const_iterator::const_iterator' requested here
471 | PWIZ_API_DECL template class BinaryData<double>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, double>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const float>' is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
| ^
pwiz/utility/misc/BinaryData.cpp:472:30: note: in instantiation of member class 'pwiz::util::BinaryData<float>::const_iterator' requested here
472 | PWIZ_API_DECL template class BinaryData<float>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, const float>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, float>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/utility/misc/BinaryData.cpp:299:14: note: in instantiation of member class 'pwiz::util::BinaryData<float>::iterator' requested here
299 | iterator begin_, end_;
| ^
pwiz/utility/misc/BinaryData.cpp:463:21: note: in instantiation of member class 'pwiz::util::BinaryData<float>::Impl' requested here
463 | binaryData._impl->makeIterator(*this, begin);
| ^
pwiz/utility/misc/BinaryData.cpp:472:30: note: in instantiation of member function 'pwiz::util::BinaryData<float>::const_iterator::const_iterator' requested here
472 | PWIZ_API_DECL template class BinaryData<float>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, float>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'iterator<std::random_access_iterator_tag, const long long>' is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
| ^
pwiz/utility/misc/BinaryData.cpp:473:30: note: in instantiation of member class 'pwiz::util::BinaryData<long long>::const_iterator' requested here
473 | PWIZ_API_DECL template class BinaryData<std::int64_t>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, const long long>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'iterator<std::random_access_iterator_tag, long long>' is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
| ^
pwiz/utility/misc/BinaryData.cpp:299:14: note: in instantiation of member class 'pwiz::util::BinaryData<long long>::iterator' requested here
299 | iterator begin_, end_;
| ^
pwiz/utility/misc/BinaryData.cpp:463:21: note: in instantiation of member class 'pwiz::util::BinaryData<long long>::Impl' requested here
463 | binaryData._impl->makeIterator(*this, begin);
| ^
pwiz/utility/misc/BinaryData.cpp:473:30: note: in instantiation of member function 'pwiz::util::BinaryData<long long>::const_iterator::const_iterator' requested here
473 | PWIZ_API_DECL template class BinaryData<std::int64_t>;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::random_access_iterator_tag, long long>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
pwiz/utility/misc/BinaryData.cpp:475:9: warning: unknown pragma ignored [-Wunknown-pragmas]
475 | #pragma managed(pop)
| ^
14 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
36 | 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'
202 | # 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]
27 | 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'
199 | # 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
27 | : 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
41 | 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'
38 | ::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
27 | : 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::string, 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
25 | 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'
38 | ::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::string, 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
50 | : 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)
42 | : 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::string, 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
85 | 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::string, 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
102 | 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::string, 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
190 | 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::string, 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
1250 | 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::string, 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
69 | 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]
29 | BOOST_HAS_TRIVIAL_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN'
193 | # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
44 | comment_char = comment_char;
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:11:
In file included from ./boost/date_time/posix_time/posix_time.hpp:24:
In file included from ./boost/date_time/posix_time/time_formatters.hpp:12:
In file included from ./boost/date_time/gregorian/gregorian.hpp:31:
In file included from ./boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from ./boost/date_time/date_facet.hpp:25:
In file included from ./boost/date_time/date_generator_parser.hpp:20:
In file included from ./boost/date_time/format_date_parser.hpp:14:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:11:
In file included from ./boost/date_time/posix_time/posix_time.hpp:24:
In file included from ./boost/date_time/posix_time/time_formatters.hpp:12:
In file included from ./boost/date_time/gregorian/gregorian.hpp:31:
In file included from ./boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from ./boost/date_time/date_facet.hpp:25:
In file included from ./boost/date_time/date_generator_parser.hpp:20:
In file included from ./boost/date_time/format_date_parser.hpp:14:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:11:
In file included from ./boost/date_time/posix_time/posix_time.hpp:24:
In file included from ./boost/date_time/posix_time/time_formatters.hpp:12:
In file included from ./boost/date_time/gregorian/gregorian.hpp:31:
In file included from ./boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from ./boost/date_time/date_facet.hpp:25:
In file included from ./boost/date_time/date_generator_parser.hpp:20:
In file included from ./boost/date_time/format_date_parser.hpp:14:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
41 | : 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'
187 | # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T)
| ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
34 | 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'
190 | # 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]
30 | 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'
196 | # 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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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:29:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
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]
41 | : 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'
187 | # 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]
36 | 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'
202 | # 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]
27 | 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'
199 | # 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
27 | : 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
41 | 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'
38 | ::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
27 | : 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::string, 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
25 | 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'
38 | ::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::string, 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
50 | : 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)
42 | : 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::string, 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
85 | 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::string, 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
102 | 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::string, 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
190 | 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::string, 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
1250 | 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::string, 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
69 | 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]
29 | BOOST_HAS_TRIVIAL_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:193:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN'
193 | # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
| ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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]
27 | 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'
199 | # 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]
65 | BOOST_HAS_NOTHROW_ASSIGN(T)
| ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
205 | # 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]
34 | 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'
190 | # 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]
30 | 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'
196 | # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T) && is_destructible<T>::value)
| ^
In file included from boost/libs/thread/src/pthread/thread.cpp:38:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
285 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from boost/libs/thread/src/pthread/thread.cpp:38:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
297 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from boost/libs/thread/src/pthread/thread.cpp:38:
In file included from ./boost/lexical_cast.hpp:32:
In file included from ./boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from ./boost/lexical_cast/detail/converter_lexical.hpp:54:
./boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
310 | sprintf(begin,
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
227 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -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/4.6/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/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 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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("MsDataHub")
>
>
> ## Catch warnings as well:
> #options(warn = 2)
>
> BiocGenerics:::testPackage("mzR")
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
Loading required namespace: XML
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
reading 143901dbb233a_7857... DONE!
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
Mass Spectrometry file handle.
Filename: 143905250ff69_7861
Number of scans: 7602
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
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see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
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.
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
RUNIT TEST PROTOCOL -- Sun Apr 12 21:07:58 2026
***********************************************
Number of test functions: 26
Number of errors: 0
Number of failures: 0
1 Test Suite :
mzR RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26
Number of errors: 0
Number of failures: 0
There were 14 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
235.051 11.618 253.031
mzR.Rcheck/mzR-Ex.timings
| name | user | system | elapsed | |
| copyWriteMSData | 4.801 | 0.445 | 5.707 | |
| isolationWindow-methods | 1.018 | 0.118 | 1.210 | |
| metadata | 0.869 | 0.142 | 1.136 | |
| mzR-class | 0.256 | 0.035 | 0.349 | |
| openMSfile | 0.622 | 0.047 | 0.785 | |
| peaks | 7.666 | 0.310 | 8.972 | |
| writeMSData | 2.828 | 0.365 | 3.217 | |