FailedConsole Output

Skipping 922 KB.. Full Log
                       ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13:0,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentDataFile.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/identdata/IdentDataFile.cpp:34:
./boost/boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from pwiz/data/identdata/IdentDataFile.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IdentData.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/IdentData.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/Reader.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Reader.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Reader.hpp:28,
                 from pwiz/data/identdata/Reader.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_protXML.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_protXML.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:28:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:28:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_pepXML.hpp:27,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/Serializer_mzid.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/Serializer_mzid.hpp:28,
                 from pwiz/data/identdata/Serializer_mzid.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/data/identdata/IO.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/IO.cpp:31:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IO.hpp:27,
                 from pwiz/data/identdata/IO.cpp:26:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/References.cpp:27:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/References.hpp:29,
                 from pwiz/data/identdata/References.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/format/alt_sstream.hpp:21,
                 from ./boost/boost/format/internals.hpp:23,
                 from ./boost/boost/format.hpp:38,
                 from ./pwiz/utility/misc/String.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/identdata/MascotReader.cpp:25:
./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
                 from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53,
                 from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34,
                 from ./boost/boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
                 from ./pwiz/utility/misc/Environment.hpp:24,
                 from ./pwiz/utility/misc/Std.hpp:29,
                 from pwiz/data/identdata/MascotReader.cpp:25:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/data/proteome/Modification.cpp:30:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     auto_ptr<Formula> formula_;
     ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
Slave went offline during the build
Build step 'Docker Build and Publish' marked build as failure
FATAL: channel is already closed
hudson.remoting.ChannelClosedException: channel is already closed
	at hudson.remoting.Channel.send(Channel.java:578)
	at hudson.remoting.Request.call(Request.java:130)
	at hudson.remoting.Channel.call(Channel.java:780)
	at hudson.Launcher$RemoteLauncher.kill(Launcher.java:953)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:540)
	at hudson.model.Run.execute(Run.java:1738)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:410)
Caused by: java.io.IOException: Unexpected termination of the channel
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:50)
Caused by: java.io.EOFException
	at java.io.ObjectInputStream$PeekInputStream.readFully(ObjectInputStream.java:2335)
	at java.io.ObjectInputStream$BlockDataInputStream.readShort(ObjectInputStream.java:2804)
	at java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:802)
	at java.io.ObjectInputStream.<init>(ObjectInputStream.java:299)
	at hudson.remoting.ObjectInputStreamEx.<init>(ObjectInputStreamEx.java:48)
	at hudson.remoting.AbstractSynchronousByteArrayCommandTransport.read(AbstractSynchronousByteArrayCommandTransport.java:34)
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:48)
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Finished: FAILURE