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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mzR
###
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* checking for file ‘mzR/DESCRIPTION’ ... OK
* preparing ‘mzR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package (it is needed to build vignettes)
      -----------------------------------
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘mzR’ ...
** this is package ‘mzR’ version ‘2.45.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppPwiz.cpp -o RcppPwiz.o
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:29:
In file included from ./pwiz/data/msdata/MSData.hpp:30:
In file included from ./pwiz/data/common/ParamTypes.hpp:29:
In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36:
In file included from ./pwiz/utility/misc/Singleton.hpp:26:
In file included from ./boost_aux/boost/utility/singleton.hpp:18:
In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32:
In file included from ./boost/function_types/function_arity.hpp:12:
In file included from ./boost/blank.hpp:26:
In file included from ./boost/type_traits/is_stateless.hpp:12:
./boost/type_traits/has_trivial_constructor.hpp:41:69: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]
   : public integral_constant <bool, ((::boost::is_pod<T>::value || BOOST_HAS_TRIVIAL_CONSTRUCTOR(T)) BOOST_TT_TRIVIAL_CONSTRUCT_FIX)>{};
                                                                    ^
./boost/type_traits/intrinsics.hpp:187:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR'
#     define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T)
                                              ^
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:29:
In file included from ./pwiz/data/msdata/MSData.hpp:30:
In file included from ./pwiz/data/common/ParamTypes.hpp:29:
In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36:
In file included from ./pwiz/utility/misc/Singleton.hpp:26:
In file included from ./boost_aux/boost/utility/singleton.hpp:18:
In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32:
In file included from ./boost/function_types/function_arity.hpp:12:
In file included from ./boost/blank.hpp:26:
In file included from ./boost/type_traits/is_stateless.hpp:13:
./boost/type_traits/has_trivial_copy.hpp:34:4: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]
   BOOST_HAS_TRIVIAL_COPY(T) BOOST_TT_TRIVIAL_CONSTRUCT_FIX
   ^
./boost/type_traits/intrinsics.hpp:190:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY'
#     define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference<T>::value)
                                        ^
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:29:
In file included from ./pwiz/data/msdata/MSData.hpp:30:
In file included from ./pwiz/data/common/ParamTypes.hpp:29:
In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36:
In file included from ./pwiz/utility/misc/Singleton.hpp:26:
In file included from ./boost_aux/boost/utility/singleton.hpp:18:
In file included from ./boost_aux/boost/utility/detail/member_dereference.hpp:32:
In file included from ./boost/function_types/function_arity.hpp:12:
In file included from ./boost/blank.hpp:26:
In file included from ./boost/type_traits/is_stateless.hpp:14:
./boost/type_traits/has_trivial_destructor.hpp:30:86: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]
template <typename T> struct has_trivial_destructor : public integral_constant<bool, BOOST_HAS_TRIVIAL_DESTRUCTOR(T)>{};
                                                                                     ^
./boost/type_traits/intrinsics.hpp:196:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR'
#     define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) (__has_trivial_destructor(T)  && is_destructible<T>::value)
                                              ^
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:30:
In file included from ./pwiz/data/msdata/Reader.hpp:29:
In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22:
In file included from ./boost/optional.hpp:15:
In file included from ./boost/optional/optional.hpp:38:
./boost/type_traits/has_nothrow_constructor.hpp:27:84: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins]
template <class T> struct has_nothrow_constructor : public integral_constant<bool, BOOST_HAS_NOTHROW_CONSTRUCTOR(T)>{};
                                                                                   ^
./boost/type_traits/intrinsics.hpp:199:48: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR'
#     define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) (__has_nothrow_constructor(T) && is_default_constructible<T>::value)
                                               ^
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:30:
In file included from ./pwiz/data/msdata/Reader.hpp:29:
In file included from ./pwiz/utility/chemistry/MzMobilityWindow.hpp:22:
In file included from ./boost/optional.hpp:15:
In file included from ./boost/optional/optional.hpp:47:
In file included from ./boost/type_traits/is_nothrow_move_assignable.hpp:16:
./boost/type_traits/has_nothrow_assign.hpp:65:7: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins]
      BOOST_HAS_NOTHROW_ASSIGN(T)
      ^
./boost/type_traits/intrinsics.hpp:205:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN'
#     define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile<T>::value && is_assignable<T&, const T&>::value)
                                          ^
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:30:
In file included from ./pwiz/data/msdata/Reader.hpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: '&&' within '||' [-Wlogical-op-parentheses]
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: note: place parentheses around the '&&' expression to silence this warning
               mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
                                                          ^
               (                                                                                        )
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:20:
./pwiz/utility/misc/Std.hpp:53:12: error: no member named 'auto_ptr' in namespace 'std'
using std::auto_ptr;
      ~~~~~^
RcppPwiz.cpp:414:57: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
        Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);
                                                      ~~       ^~~~~~~
                                                      %zu
RcppPwiz.cpp:788:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
    if ( (precursorScanNum[i] > 0) | (precursorMZ[i] > 0) ) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
RcppPwiz.cpp:788:10: note: cast one or both operands to int to silence this warning
RcppPwiz.cpp:885:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Index whichChrom out of bounds [1 ... %d].\n", (clp->size()));
                                                     ~~       ^~~~~~~~~~~~~
                                                     %zu
9 warnings and 1 error generated.
make: *** [RcppPwiz.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp80ZsN6/Rinst3bdf43a07d7c/mzR’
      -----------------------------------
ERROR: package installation failed