mzR

Package: mzR
Type: Package
Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
(mass spectrometry data)
Version: 2.6.2
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
Steffen Neumann <sneumann@ipb-halle.de>,
Laurent Gatto <lg390@cam.ac.uk>,
Qiang Kou <qkou@umail.iu.edu>
Description: mzR provides a unified API to the common file formats and
parsers available for mass spectrometry data. It comes with a
wrapper for the ISB random access parser for mass spectrometry
mzXML, mzData and mzML files. The package contains the
original code written by the ISB, and a subset of the
proteowizard library for mzML and mzIdentML. The netCDF
reading code has previously been used in XCMS.
License: Artistic-2.0
LazyLoad: yes
Depends: Rcpp (>= 0.10.1), methods, utils
Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics
Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr
VignetteBuilder: knitr
LinkingTo: Rcpp, zlibbioc
RcppModules: Ramp, Pwiz, Ident
SystemRequirements: C++11, GNU make, NetCDF
URL: https://github.com/sneumann/mzR/
BugReports: https://github.com/sneumann/mzR/issues/
biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
MassSpectrometry
NeedsCompilation: yes
Packaged: 2016-05-16 03:09:16 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/Version.o ./pwiz/data/identdata/References.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o rampR.o R_init_mzR.o
find . -name *~ -exec rm {} ;   ## from cleanup
find . -name *.o -exec rm {} ;  ## from cleanup
find . -name "#*#" -exec rm {} ; ## from cleanup
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c cramp.cpp -o cramp.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp.cpp -o ramp.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c rnetCDF.c -o rnetCDF.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./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 RcppPwiz.h:19,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:22,
                 from RcppPwiz.cpp:1:
./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/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./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 RcppPwiz.h:19,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:22,
                 from RcppPwizModule.cpp:2:
./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/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from ./pwiz/data/proteome/Digestion.hpp:33,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:36,
                 from ./pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from ./pwiz/data/proteome/Digestion.hpp:33,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentDataFile.hpp:29,
                 from RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:538:34: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:547:34: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
./boost/smart_ptr/shared_ptr.hpp:549:38: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost -Wno-deprecated-register `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
./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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/detail/shared_count.hpp:396:33: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:249:65: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:448:31: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:461:22: 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++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost