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###
### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL mzR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘mzR’ ...
** using staged installation
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.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
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-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c cramp.cpp -o cramp.o
In file included from cramp.cpp:49:0:
cramp.h: In constructor ‘cRamp::cRamp(const char*, bool)’:
cramp.h:149:10: warning: ‘cRamp::m_declaredScansOnly’ will be initialized after [-Wreorder]
bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans
^~~~~~~~~~~~~~~~~~~
cramp.h:148:18: warning: ‘rampRunInfo* cRamp::m_runInfo’ [-Wreorder]
rampRunInfo *m_runInfo; // scan count etc
^~~~~~~~~
cramp.cpp:72:1: warning: when initialized here [-Wreorder]
cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from ramp.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
ramp.cpp: In function ‘RAMPFILE* rampOpenFile(const char*)’:
ramp.cpp:248:23: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
^~~~
ramp.cpp: In function ‘ramp_fileoffset_t getIndexOffset(RAMPFILE*)’:
ramp.cpp:451:12: warning: unused variable ‘nread’ [-Wunused-variable]
size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
^~~~~
ramp.cpp: In function ‘ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)’:
ramp.cpp:650:31: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^~~~
ramp.cpp:692:31: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^~~~
ramp.cpp:729:27: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^~~~
ramp.cpp: In function ‘void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)’:
ramp.cpp:1446:27: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp: In function ‘int readMsLevel(RAMPFILE*, ramp_fileoffset_t)’:
ramp.cpp:1532:15: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp:1528:11: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp: In function ‘char* rampConstructInputPath(char*, int, const char*, const char*)’:
ramp.cpp:1744:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j= 0; j< g.gl_pathc; j++) // for each file in directory
~^~~~~~~~~~~~
ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
ramp.cpp:2090:28: warning: unused variable ‘nread’ [-Wunused-variable]
size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
^~~~~
ramp.cpp:2293:27: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
^~~~
ramp.cpp:2340:24: warning: unused variable ‘nread’ [-Wunused-variable]
size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
^~~~~
ramp.cpp:2394:21: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
int err;
^~~
ramp.cpp:2212:19: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
^~~~
ramp.cpp: In function ‘void readMSRun(RAMPFILE*, RunHeaderStruct*)’:
ramp.cpp:2520:15: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp:2544:15: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp:2516:11: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp: In function ‘InstrumentStruct* getInstrumentStruct(RAMPFILE*)’:
ramp.cpp:2695:19: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp:2731:19: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
ramp.cpp:2682:11: warning: unused variable ‘fgot’ [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function ‘Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()’:
RcppRamp.cpp:215:27: warning: unused variable ‘info’ [-Wunused-variable]
rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
^~~~
RcppRamp.cpp: In member function ‘Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector, double, double, double)’:
RcppRamp.cpp:388:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < scanNumbers.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppRampModule.cpp -o RcppRampModule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/boost/iostreams/chain.hpp:256:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwiz.h:4,
from RcppPwiz.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getScanHeaderInfo(Rcpp::IntegerVector)’:
RcppPwiz.cpp:173:11: warning: unused variable ‘N’ [-Wunused-variable]
int N = slp->size();
^
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(int)’:
RcppPwiz.cpp:366:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((whichScan <= 0) || (whichScan > slp->size()))
~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:380:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pairs.size(); i++)
~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)’:
RcppPwiz.cpp:732:29: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’:
RcppPwiz.cpp:807:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
} else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:817:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pairs.size(); i++) {
~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo(Rcpp::IntegerVector)’:
RcppPwiz.cpp:837:10: warning: unused variable ‘nativeIdFormat_’ [-Wunused-variable]
CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this...
^~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector, double, double, double)’:
RcppPwiz.cpp:968:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < scanNumbers.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:974:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k < pairs.size(); k++)
~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/boost/iostreams/chain.hpp:256:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppPwizModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdent.h:4,
from RcppIdent.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
RcppIdent.cpp: In member function ‘Rcpp::DataFrame RcppIdent::getScore()’:
RcppIdent.cpp:287:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < nCvParams; j++) {
~~^~~~~~~~~~~
RcppIdent.cpp: In member function ‘Rcpp::List RcppIdent::getPara()’:
RcppIdent.cpp:376:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppIdent.cpp:382:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RcppIdentModule.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 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++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
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++/7/bits/unique_ptr.h:51:28: note: declared here
template 