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CHECK report for mzR on malbec2

This page was generated on 2018-10-17 08:23:49 -0400 (Wed, 17 Oct 2018).

Package 976/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.14.0
Steffen Neumann
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/mzR
Branch: RELEASE_3_7
Last Commit: bf1154b
Last Changed Date: 2018-04-30 10:35:21 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mzR
Version: 2.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings mzR_2.14.0.tar.gz
StartedAt: 2018-10-16 02:17:43 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:19:12 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 88.9 seconds
RetCode: 0
Status:  OK 
CheckDir: mzR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings mzR_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/mzR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 99.0Mb
  sub-directories of 1Mb or more:
    libs  98.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘Rhdf5lib’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/mzR/libs/mzR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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

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

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/mzR.Rcheck/00check.log’
for details.

Installation output

mzR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL mzR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/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/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.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=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c cramp.cpp -o cramp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c ramp.cpp -o ramp.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rnetCDF.c -o rnetCDF.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppPwiz.h:20,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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:20,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwiz.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppPwiz.h:20,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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:20,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:23,
                 from RcppPwizModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppIdent.cpp -o RcppIdent.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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:14,
                 from RcppIdent.cpp:1:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:11,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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/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 RcppIdent.h:14,
                 from RcppIdentModule.cpp:2:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-bioc/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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from boost/libs/regex/src/fileiter.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from boost/libs/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex.hpp:32,
                 from ./boost/boost/regex.hpp:31,
                 from boost/libs/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/wc_regex_traits.cpp:76:
./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++/5/memory:81:0,
                 from boost/libs/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/libs/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/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/regex/v4/regex_workaround.hpp:43,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost/boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/boost/regex/regex_traits.hpp:27,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/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/iostreams/filter/symmetric.hpp:60,
                 from ./boost/boost/iostreams/filter/zlib.hpp:31,
                 from boost/libs/iostreams/src/zlib.cpp:19:
./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++/5/memory:81:0,
                 from ./boost/boost/iostreams/filter/zlib.hpp:20,
                 from boost/libs/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.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/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/libs/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/filesystem/path_traits.hpp:29,
                 from ./boost/boost/filesystem/path.hpp:25,
                 from boost/libs/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/common/MemoryIndex.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/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/common/MemoryIndex.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/common/CVTranslator.cpp:29:
./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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/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/common/CVTranslator.cpp:29:
./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++/5/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/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/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/common/cv.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/common/cv.cpp:34:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/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/common/ParamTypes.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/ParamTypes.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/common/BinaryIndexStream.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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/common/BinaryIndexStream.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/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 pwiz/data/common/BinaryIndexStream.cpp:27:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/data/common/Index.hpp:29,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/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/data/common/diff_std.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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_aux/boost/enum/bitfield.hpp:22,
                 from ./boost_aux/boost/enum.hpp:20,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
./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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/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/common/Unimod.cpp:26:
./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++/5/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/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/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/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Connection_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/../MSData.hpp:29,
                 from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
                 from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/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/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/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/boost/smart_ptr.hpp:19,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/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/boost/smart_ptr.hpp:19,
                 from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:27,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/msdata/mz5/../../common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/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/SpectrumList_MGF.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/DefaultReaderList.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/ChromatogramListBase.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
                 from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/ChromatogramList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/ChromatogramList_mz5.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/msdata/examples.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/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/msdata/examples.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/examples.hpp:29,
                 from pwiz/data/msdata/examples.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mzML.cpp:33:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mzML.cpp:33:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_MSn.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:26,
                 from pwiz/data/msdata/Serializer_MSn.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/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/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28,
                 from pwiz/data/msdata/Reader.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/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/msdata/Serializer_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/Serializer_mz5.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_MGF.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_MGF.hpp:27,
                 from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_mzXML.cpp:33:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/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/msdata/Serializer_mzXML.cpp:34:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mzML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/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/SpectrumList_mzML.cpp:32:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_MSn.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/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/SpectrumList_MSn.cpp:31:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_mz5.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/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/SpectrumList_mz5.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/SpectrumList_mz5.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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 pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/iostreams/copy.hpp:26,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:32:
./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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/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/msdata/BinaryDataEncoder.cpp:38:
./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++/5/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/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/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/msdata/Diff.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Diff.hpp:29,
                 from pwiz/data/msdata/Diff.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/msdata/MSData.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/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/msdata/MSData.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/msdata/References.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/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/msdata/References.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/References.hpp:29,
                 from pwiz/data/msdata/References.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/msdata/SpectrumList_mzXML.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/msdata/SpectrumList_mzXML.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/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/SpectrumList_mzXML.cpp:30:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/msdata/IO.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/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/msdata/IO.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/IO.hpp:29,
                 from pwiz/data/msdata/IO.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_BTDX.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumList_BTDX.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/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/SpectrumList_BTDX.cpp:30:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/msdata/SpectrumInfo.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/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/msdata/SpectrumInfo.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.hpp:29,
                 from pwiz/data/msdata/SpectrumInfo.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/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/msdata/RAMPAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from ./random_access_gzFile.h:21,
                 from ./ramp.h:72,
                 from pwiz/data/msdata/RAMPAdapter.hpp:29,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/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/msdata/LegacyAdapter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/LegacyAdapter.hpp:30,
                 from pwiz/data/msdata/LegacyAdapter.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumIterator.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/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/msdata/SpectrumIterator.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.hpp:29,
                 from pwiz/data/msdata/SpectrumIterator.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/msdata/MSDataFile.cpp:36:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/msdata/MSDataFile.cpp:37:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/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/msdata/MSDataFile.cpp:41:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/multi_index/sequenced_index.hpp:49,
                 from ./pwiz/utility/misc/mru_list.hpp:30,
                 from pwiz/data/msdata/MemoryMRUCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.hpp:28,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/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/msdata/SpectrumListCache.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/SpectrumListCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/msdata/Index_mzML.cpp:25:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/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/msdata/Index_mzML.cpp:25:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/data/common/ParamTypes.hpp:29,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Index_mzML.hpp:28,
                 from pwiz/data/msdata/Index_mzML.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/msdata/SpectrumWorkerThreads.cpp:24:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/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++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/proteome/Digestion.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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/Digestion.cpp:32:
./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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/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/Digestion.cpp:32:
./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++/5/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/proteome/Digestion.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/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/Peptide.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++/5/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/Peptide.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/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/AminoAcid.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++/5/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/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/utility/minimxml/XMLWriter.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/utility/minimxml/XMLWriter.cpp:26:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/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/utility/minimxml/XMLWriter.cpp:27:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/XMLWriter.hpp:29,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/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/utility/minimxml/SAXParser.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.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/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/utility/minimxml/SAXParser.cpp:29:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/minimxml/SAXParser.hpp:31,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/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/utility/chemistry/Chemistry.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++/5/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/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.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++/5/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/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/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/utility/chemistry/MZTolerance.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/chemistry/MZTolerance.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/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/utility/misc/IntegerSet.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IntegerSet.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/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/utility/misc/Base64.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/Base64.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/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/utility/misc/IterationListener.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/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/utility/misc/IterationListener.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/utility/misc/MSIHandler.cpp:25:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/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/utility/misc/MSIHandler.cpp:25:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/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/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/algorithm/string/classification.hpp:15,
                 from ./boost/boost/algorithm/string/trim.hpp:23,
                 from ./boost/boost/algorithm/string.hpp:19,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/Filesystem.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/utility/misc/TabReader.cpp:25:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/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/utility/misc/TabReader.cpp:25:
./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++/5/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/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/utility/misc/random_access_compressed_ifstream.cpp:82:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/utility/misc/random_access_compressed_ifstream.cpp:82:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/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/utility/misc/random_access_compressed_ifstream.cpp:83:
./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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/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/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./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++/5/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/utility/misc/SHA1Calculator.cpp:33:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/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/utility/misc/SHA1Calculator.cpp:33:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/utility/misc/unit.hpp:30,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/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/utility/misc/sha1calc.cpp:26:
./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++/5/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/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/pthread/once_atomic.hpp:19,
                 from ./boost/boost/thread/once.hpp:20,
                 from boost/libs/thread/src/pthread/./once_atomic.cpp:9,
                 from boost/libs/thread/src/pthread/once.cpp:8:
./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++/5/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/get_pointer.hpp:14,
                 from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/pthread/once_atomic.hpp:19,
                 from ./boost/boost/thread/once.hpp:20,
                 from boost/libs/thread/src/pthread/./once_atomic.cpp:9,
                 from boost/libs/thread/src/pthread/once.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/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/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/detail/thread.hpp:30,
                 from ./boost/boost/thread/thread_only.hpp:22,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./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++/5/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 ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -c rampR.cpp -o rampR.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG `nc-config --cflags || /bin/true`   -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_mzR.c -o R_init_mzR.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/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/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/mzR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzR)

Tests output

mzR.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> library("mzR")
Loading required package: Rcpp
> library("msdata")
> 
> BiocGenerics:::testPackage("mzR")
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Mass Spectrometry file handle.
Filename:  MM14.mzdata 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzdata.gz 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  MM14.mzML 
Number of scans:  112 
Mass Spectrometry file handle.
Filename:  threonine_i2_e35_pH_tree.mzXML 
Number of scans:  55 
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].
Index whichScan out of bounds [1 ... 0].


RUNIT TEST PROTOCOL -- Tue Oct 16 02:19:10 2018 
*********************************************** 
Number of test functions: 34 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 34 test functions, 0 errors, 0 failures
Number of test functions: 34 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 45.544   0.972  47.583

Example timings

mzR.Rcheck/mzR-Ex.timings

nameusersystemelapsed
copyWriteMSData0.1560.0080.191
isolationWindow-methods1.1640.1041.266
metadata0.1680.0080.262
mzR-class0.0520.0120.062
openMSfile0.1480.0040.154
peaks1.1240.0201.144
writeMSData0.0960.0040.097