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This page was generated on 2024-02-27 11:37:49 -0500 (Tue, 27 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1382/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.36.0  (landing page)
Steffen Neumann
Snapshot Date: 2024-02-26 14:53:20 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/mzR
git_branch: RELEASE_3_18
git_last_commit: 1764563
git_last_commit_date: 2023-10-24 09:47:39 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for mzR on lconway


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.

raw results


Summary

Package: mzR
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mzR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mzR_2.36.0.tar.gz
StartedAt: 2024-02-26 22:37:52 -0500 (Mon, 26 Feb 2024)
EndedAt: 2024-02-26 22:39:44 -0500 (Mon, 26 Feb 2024)
EllapsedTime: 111.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mzR.Rcheck
Warnings: 2

Command output

##############################################################################
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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_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/mzR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr<pwiz::chemistry::Formula>' is deprecated [-Wdeprecated-declarations]
  pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/mzR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
* 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 R 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/mzR/libs/mzR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

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

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

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/mzR.Rcheck/00check.log’
for details.



Installation output

mzR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:30:
In file included from ./pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:30:
In file included from ./pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppIdent.cpp -o RcppIdent.o
In file included from RcppIdent.cpp:1:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from RcppIdentModule.cpp:2:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:25:
In file included from pwiz/data/common/MemoryIndex.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/detail/shared_count.hpp:27:
In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27:
In file included from ./boost/checked_delete.hpp:15:
./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::MemoryIndex::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete x;
    ^
./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::MemoryIndex::Impl>' requested here
            boost::checked_delete( p );
                   ^
./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::MemoryIndex::Impl>' requested here
    boost::detail::shared_count( p ).swap( pn );
    ^
./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::MemoryIndex::Impl, pwiz::data::MemoryIndex::Impl>' requested here
        boost::detail::sp_pointer_construct( this, p, pn );
                       ^
pwiz/data/common/MemoryIndex.cpp:73:44: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::MemoryIndex::Impl>::shared_ptr<pwiz::data::MemoryIndex::Impl>' requested here
PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
                                           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp:145:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ~~
pwiz/data/common/CVTranslator.cpp:145:53: note: place parentheses around the '&&' expression to silence this warning
    return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
                                                    ^
            (                                                       )
pwiz/data/common/CVTranslator.cpp:146:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:146:40: note: place parentheses around the '&&' expression to silence this warning
            key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
                                       ^
            (                                        )
pwiz/data/common/CVTranslator.cpp:147:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:147:40: note: place parentheses around the '&&' expression to silence this warning
            key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
                                       ^
            (                                        )
pwiz/data/common/CVTranslator.cpp:148:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:148:40: note: place parentheses around the '&&' expression to silence this warning
            key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
                                       ^
            (                                          )
4 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:25:
In file included from pwiz/data/common/BinaryIndexStream.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/detail/shared_count.hpp:27:
In file included from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27:
In file included from ./boost/checked_delete.hpp:15:
./boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'pwiz::data::BinaryIndexStream::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete x;
    ^
./boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::BinaryIndexStream::Impl>' requested here
            boost::checked_delete( p );
                   ^
./boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::BinaryIndexStream::Impl>' requested here
    boost::detail::shared_count( p ).swap( pn );
    ^
./boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::BinaryIndexStream::Impl, pwiz::data::BinaryIndexStream::Impl>' requested here
        boost::detail::sp_pointer_construct( this, p, pn );
                       ^
pwiz/data/common/BinaryIndexStream.cpp:417:82: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::BinaryIndexStream::Impl>::shared_ptr<pwiz::data::BinaryIndexStream::Impl>' requested here
PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
                                                                                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:25:
In file included from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32:
In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:31:
In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:32:
In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:29:
In file included from pwiz/data/msdata/DefaultReaderList.hpp:29:
In file included from pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:28:
In file included from pwiz/data/msdata/ChromatogramList_mz5.hpp:31:
In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31:
In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
pwiz/data/msdata/Serializer_MSn.cpp:44:11: warning: unused variable 'sizeChargeMSn' [-Wunused-const-variable]
const int sizeChargeMSn    = 12; // struct Charge{ int z; double mass; }
          ^
pwiz/data/msdata/Serializer_MSn.cpp:45:11: warning: unused variable 'sizePeakMSn' [-Wunused-const-variable]
const int sizePeakMSn      = 12; // struct Peak{ double mz; float intensity; }
          ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:28:
In file included from pwiz/data/msdata/Serializer_mz5.hpp:32:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:31:
./boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
BOOST_PRAGMA_MESSAGE(
^
./boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:43:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:28:
In file included from pwiz/data/msdata/SpectrumList_mz5.hpp:31:
In file included from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31:
In file included from pwiz/data/msdata/mz5/Connection_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28:
In file included from pwiz/data/msdata/mz5/../MSDataFile.hpp:30:
In file included from pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
pwiz/data/msdata/MSData.cpp:1115:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp:2132:35: warning: '&&' within '||' [-Wlogical-op-parentheses]
            else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                     ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~                ~~
pwiz/data/msdata/IO.cpp:2132:35: note: place parentheses around the '&&' expression to silence this warning
            else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                                  ^
                     (                                        )
pwiz/data/msdata/IO.cpp:2836:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
        else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                ~~
pwiz/data/msdata/IO.cpp:2836:31: note: place parentheses around the '&&' expression to silence this warning
        else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                              ^
                 (                                            )
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
pwiz/data/msdata/SpectrumList_BTDX.cpp:279:19: warning: private field 'msd_' is not used [-Wunused-private-field]
    const MSData& msd_;
                  ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (done() && &that.spectrumList_==&pastEndMarker_ ||
            ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
pwiz/data/msdata/SpectrumIterator.cpp:125:20: note: place parentheses around the '&&' expression to silence this warning
    return (done() && &that.spectrumList_==&pastEndMarker_ ||
                   ^
            (                                             )
pwiz/data/msdata/SpectrumIterator.cpp:126:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
            &spectrumList_==&pastEndMarker_ && that.done() ||
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:126:45: note: place parentheses around the '&&' expression to silence this warning
            &spectrumList_==&pastEndMarker_ && that.done() ||
                                            ^
            (                                             )
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
            &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: note: place parentheses around the '&&' expression to silence this warning
            &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
                                                ^
            (                                                                       )
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
           ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
pwiz/data/msdata/SpectrumIterator.cpp:141:34: note: place parentheses around the '&&' expression to silence this warning
    return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
                                 ^
           (                                                              )
4 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:30:
In file included from pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from pwiz/data/identdata/IdentDataFile.cpp:25:
In file included from pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:31:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:29:
In file included from pwiz/data/identdata/DefaultReaderList.hpp:29:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from pwiz/data/identdata/Reader.cpp:26:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from pwiz/data/identdata/Serializer_protXML.cpp:28:
In file included from pwiz/data/identdata/Serializer_protXML.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder-ctor]
        strict(strict),
        ^~~~~~~~~~~~~~
        SourceFilesPtr(returnValueSourceFiles)
pwiz/data/identdata/Serializer_protXML.cpp:476:10: warning: private field 'readSpectrumQueries' is not used [-Wunused-private-field]
    bool readSpectrumQueries;
         ^
pwiz/data/identdata/Serializer_protXML.cpp:477:38: warning: private field 'ilr' is not used [-Wunused-private-field]
    const IterationListenerRegistry* ilr;
                                     ^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from pwiz/data/identdata/Serializer_pepXML.cpp:25:
In file included from pwiz/data/identdata/Serializer_pepXML.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/Serializer_pepXML.cpp:561:104: warning: adding 'char' to a string does not append to the string [-Wstring-plus-int]
                        default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
                                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pwiz/data/identdata/Serializer_pepXML.cpp:561:104: note: use array indexing to silence this warning
                        default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
                                                                                                       ^
                                                     &                                                 [   ]
pwiz/data/identdata/Serializer_pepXML.cpp:1546:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
    }
    ^
pwiz/data/identdata/Serializer_pepXML.cpp:995:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1450:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1796:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1970:38: warning: private field 'ilr' is not used [-Wunused-private-field]
    const IterationListenerRegistry* ilr;
                                     ^
7 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from pwiz/data/identdata/Serializer_mzid.cpp:26:
In file included from pwiz/data/identdata/Serializer_mzid.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from pwiz/data/identdata/IO.cpp:26:
In file included from pwiz/data/identdata/IO.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from pwiz/data/identdata/References.cpp:25:
In file included from pwiz/data/identdata/References.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
            BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(c.get())->affiliations)
            ^
./boost/foreach.hpp:1107:108: note: expanded from macro 'BOOST_FOREACH'
    if (boost::foreach_detail_::auto_any_t BOOST_FOREACH_ID(_foreach_col) = BOOST_FOREACH_CONTAIN(COL)) {} else   \
                                                                                                           ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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:26:
In file included from pwiz/data/identdata/MascotReader.hpp:28:
In file included from ./pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
In file included from pwiz/data/identdata/MascotReader.cpp:26:
pwiz/data/identdata/MascotReader.hpp:62:11: warning: private field 'pimpl' is not used [-Wunused-private-field]
    Impl* pimpl;
          ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from pwiz/data/proteome/Modification.cpp:27:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/proteome/Modification.cpp:89:5: warning: 'auto_ptr<pwiz::chemistry::Formula>' is deprecated [-Wdeprecated-declarations]
    auto_ptr<Formula> formula_;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<pwiz::chemistry::Formula>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from pwiz/data/proteome/Digestion.cpp:27:
In file included from pwiz/data/proteome/Digestion.hpp:32:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from pwiz/data/proteome/Peptide.cpp:26:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::key_compare, pwiz::util::virtual_map<int, pwiz::proteome::ModificationList>::allocator_type> &' (aka 'virtual_map<int, pwiz::proteome::ModificationList, std::less<int>, std::allocator<std::pair<const int, pwiz::proteome::ModificationList>>> &') vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ~~
pwiz/utility/misc/IntegerSet.cpp:307:63: note: place parentheses around the '&&' expression to silence this warning
    return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
                                                              ^
            (                                                                       )
pwiz/utility/misc/IntegerSet.cpp:308:23: warning: '&&' within '||' [-Wlogical-op-parentheses]
            it_==end_ && that.it_==nothing_.end());
            ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/IntegerSet.cpp:308:23: note: place parentheses around the '&&' expression to silence this warning
            it_==end_ && that.it_==nothing_.end());
                      ^
            (                                    )
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
pwiz/utility/misc/BinaryData.cpp:303:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma managed(push, off)
        ^
pwiz/utility/misc/BinaryData.cpp:475:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma managed(pop)
        ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
        comment_char = comment_char;
                     ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output

mzR.Rcheck/tests/runTests.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

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


RUNIT TEST PROTOCOL -- Mon Feb 26 22:39:35 2024 
*********************************************** 
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
3: In XML::xmlTreeParse(system.file("extdata", "mzXML_idx_3.2.xsd.xml",  :
  NULL value for external reference
> 
> proc.time()
   user  system elapsed 
 32.930   2.991  39.190 

Example timings

mzR.Rcheck/mzR-Ex.timings

nameusersystemelapsed
copyWriteMSData0.1370.0210.154
isolationWindow-methods1.1170.1291.280
metadata0.2390.0520.298
mzR-class0.0430.0140.058
openMSfile0.0700.0110.082
peaks0.8060.0860.910
writeMSData0.0860.0190.100