mzR installation error in Raspberry Pi 4

[adelomana]

Hello.

I’m trying to install mzR on a Raspberry Pi 4, and I’m struggling with it. Frankly, I'm very stuck and I don't know how to move forward.

I'm suspicious about: the compiler? Or maybe there is a problem with boost libraries? Something else? Would it be better to use another version?

Here is some info about the error, any help would be really appreciated.

Thank you so much!!!

flatey 2020-11-12 13:40:36 ~ : R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
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> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager") 
> BiocManager::install("mzR")
Bioconductor version 3.8 (BiocManager 1.30.10), R 3.5.2 (2018-12-20)
Installing package(s) 'mzR'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/mzR_2.16.2.tar.gz'
Content type 'application/x-gzip' length 4912521 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

* installing *source* package ‘mzR’ ...
** 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"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cramp.cpp -o cramp.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ramp_base64.cpp -o ramp_base64.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ramp.cpp -o ramp.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppRamp.cpp -o RcppRamp.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppRampModule.cpp -o RcppRampModule.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included 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/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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17,
                 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++/8/bits/locale_conv.h:41,
                 from /usr/include/c++/8/locale:43,
                 from /usr/include/c++/8/iomanip:43,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/RcppCommon.h:52,
                 from /home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = boost::filesystem::detail::dir_itr_imp]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = boost::filesystem::detail::dir_itr_imp; Y = boost::filesystem::detail::dir_itr_imp]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = boost::filesystem::detail::dir_itr_imp; T = boost::filesystem::detail::dir_itr_imp]’
./boost/boost/filesystem/operations.hpp:805:40:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::dir_itr_imp>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::dir_itr_imp>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = boost::filesystem::detail::recur_dir_itr_imp]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = boost::filesystem::detail::recur_dir_itr_imp; Y = boost::filesystem::detail::recur_dir_itr_imp]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = boost::filesystem::detail::recur_dir_itr_imp; T = boost::filesystem::detail::recur_dir_itr_imp]’
./boost/boost/filesystem/operations.hpp:1048:44:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::recur_dir_itr_imp>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::recur_dir_itr_imp>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::msdata::Software]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::msdata::Software; Y = pwiz::msdata::Software]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::msdata::Software; T = pwiz::msdata::Software]’
RcppPwiz.cpp:554:36:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<pwiz::msdata::Software>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<pwiz::msdata::Software>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::msdata::DataProcessing]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::msdata::DataProcessing; Y = pwiz::msdata::DataProcessing]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::msdata::DataProcessing; T = pwiz::msdata::DataProcessing]’
RcppPwiz.cpp:567:55:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<pwiz::msdata::DataProcessing>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<pwiz::msdata::DataProcessing>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::msdata::SpectrumListSimple]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::msdata::SpectrumListSimple; Y = pwiz::msdata::SpectrumListSimple]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::msdata::SpectrumListSimple; T = pwiz::msdata::SpectrumListSimple]’
RcppPwiz.cpp:649:69:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<pwiz::msdata::SpectrumListSimple>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<pwiz::msdata::SpectrumListSimple>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::msdata::Spectrum]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::msdata::Spectrum; Y = pwiz::msdata::Spectrum]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::msdata::Spectrum; T = pwiz::msdata::Spectrum]’
RcppPwiz.cpp:655:61:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<pwiz::msdata::Spectrum>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<pwiz::msdata::Spectrum>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::msdata::BinaryDataArray]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::msdata::BinaryDataArray; Y = pwiz::msdata::BinaryDataArray]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::msdata::BinaryDataArray; T = pwiz::msdata::BinaryDataArray]’
RcppPwiz.cpp:745:51:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<pwiz::msdata::BinaryDataArray>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<pwiz::msdata::BinaryDataArray>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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: In instantiation of ‘boost::detail::shared_count::shared_count(Y*) [with Y = boost::filesystem::filesystem_error::m_imp]’:
./boost/boost/smart_ptr/shared_ptr.hpp:271:20:   required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = boost::filesystem::filesystem_error::m_imp; Y = boost::filesystem::filesystem_error::m_imp]’
./boost/boost/smart_ptr/shared_ptr.hpp:349:44:   required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = boost::filesystem::filesystem_error::m_imp; T = boost::filesystem::filesystem_error::m_imp]’
./boost/boost/smart_ptr/shared_ptr.hpp:620:9:   required from ‘void boost::shared_ptr<T>::reset(Y*) [with Y = boost::filesystem::filesystem_error::m_imp; T = boost::filesystem::filesystem_error::m_imp]’
./boost/boost/filesystem/operations.hpp:82:36:   required from here
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<boost::filesystem::filesystem_error::m_imp>’
             pi_ = new sp_counted_impl_p<Y>( p );
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 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/sp_counted_impl.hpp:53:25: note:   because the following virtual functions are pure within ‘boost::detail::sp_counted_impl_p<boost::filesystem::filesystem_error::m_imp>’:
 template<class X> class sp_counted_impl_p: public sp_counted_base
                         ^~~~~~~~~~~~~~~~~
In file included from ./boost/boost/smart_ptr/detail/sp_counted_base.hpp:72,
                 from ./boost/boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:28,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:112:20: note:  ‘virtual void* boost::detail::sp_counted_base::get_local_deleter(const sp_typeinfo&)’
     virtual void * get_local_deleter( sp_typeinfo const & ti ) = 0;
                    ^~~~~~~~~~~~~~~~~
make: *** [/usr/lib/R/etc/Makeconf:171: RcppPwiz.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/mzR’

The downloaded source packages are in
    ‘/tmp/RtmpMbmCAg/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class,
  cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet,
  rpart, spatial, survival
Warning message:
In install.packages(...) :
  installation of package ‘mzR’ had non-zero exit status
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: arm-unknown-linux-gnueabihf (32-bit)
Running under: Raspbian GNU/Linux 10 (buster)

Matrix products: default
BLAS: /usr/lib/arm-linux-gnueabihf/openblas/libblas.so.3
LAPACK: /usr/lib/arm-linux-gnueabihf/libopenblas_armv6p-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.5.2      tools_3.5.2        

[sneumann]

Hi, so it seems this is indeed a C++ compiler error:

g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o
...
./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::dir_itr_imp>’
...
make: *** [/usr/lib/R/etc/Makeconf:171: RcppPwiz.o] Error 1

I don't have an immediate solution. If possible, can you try to compile the branch with the new boost/pwiz in https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_20290 ? I didn't merge that branch yet, as it SEGV when reading the data, but it would be interesting to know if that at least compiles for you.

Yours, Steffen

[adelomana]

Hi Stefen.

Thanks for your response. I tried that new version but I got some errors. Not sure it is the same (see below). BTW, I updated the R version and installed other packages, but still, it is on a Raspberry Pi 4.

Also, I managed to get access to a more powerful Intel-based machine. I installed mzR there with no problems. I'm very glad to be using it now there. So I'm not so worried about this error, feel free to close the issue if it's too much trouble, I'm happy to use mzR on the other machine, no need to install it on the Raspberry for me...

Cheers.

pi@raspberrypi:~ $ R

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: armv7l-unknown-linux-gnueabihf (32-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.

Natural language support but running in an English locale

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('devtools') Loading required package: usethis install('/home/pi/Downloads/mzR-feature-updatePwiz_3_0_20290') ✔ checking for file ‘/home/pi/Downloads/mzR-feature-updatePwiz_3_0_20290/DESCRIPTION’ (1.4s) ─ preparing ‘mzR’: (44.1s) ✔ checking DESCRIPTION meta-information ─ cleaning src ─ running ‘cleanup’ (625ms) ─ checking for LF line-endings in source and make files and shell scripts (4.8s) ─ checking for empty or unneeded directories (1m 9.7s) Removed empty directory ‘mzR/src/boost/libs/predef/tools’ ─ building ‘mzR_2.23.1.1.tar.gz’ (1.9s) Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/collectors/laps_accumulator_set.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/collectors/laps_sequence_container.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/accumulator_set_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/elapsed_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/times_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/clock_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/laps_accumulator_set_stopwatch_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/laps_stopwatch_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/process_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/stopwatch_reporter_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/stopwatch_reporter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/strict_stopclock.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/system_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/thread_default_formatter.hpp’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/filesystem/example/msvc/directory_symlink_parent_resolution/directory_symlink_parent_resolution.vcxproj’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/geometry/example/with_external_libs/contrib/shapelib-1.3.0b2/boost_geometry_readme.txt’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/intrusive/proj/vc7ide/has_member_function_callable_with/has_member_function_callable_with.vcproj’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/intrusive/proj/vc7ide/has_member_function_callable_with_no_decltype/has_member_function_callable_with_no_decltype.vcproj’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘mzR/src/boost/libs/intrusive/proj/vc7ide/has_member_function_callable_with_no_variadic/has_member_function_callable_with_no_variadic.vcproj’

Running /usr/local/lib/R/bin/R CMD INSTALL \ /tmp/Rtmp6ZfNOB/mzR_2.23.1.1.tar.gz --install-tests

• installing to library ‘/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0’
• installing source package ‘mzR’ ... using staged installation libs rm -f cramp.o ramp_base64.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/SpectrumListBase.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 ./pwlizer_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/ramp/ramp.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c cramp.cpp -o cramp.o g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c RcppRamp.cpp -o RcppRamp.o g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include' -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o In file included from /usr/include/c++/8/vector:69, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator<double, std::vector >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = pwiz::util::BinaryData::iterator; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘gnu_cxx::__normal_iterator<double, std::vector >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~ In file included from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:178, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h: In function ‘SEXPREC Rcpp::internal::primitive_range_wrapimplnocast(InputIterator, InputIterator, std::random_access_iterator_tag) [with InputIterator = __gnu_cxx::normal_iterator<const double, std::vector >; T = double]’: /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:112:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const double, std::vector >’ changed in GCC 7.1 inline SEXP primitive_range_wrapimplnocast(InputIterator first, InputIterator last, ^~~~~~~~~~ /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:112:21: note: parameter passing for argument of type ‘gnu_cxx::__normal_iterator<const double*, std::vector >’ changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’: /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘gnu_cxx::normal_iterator<double*, std::vector >’} changed in GCC 7.1 _M_range_insert(pos, first, last, ^~~~~~~ In file included from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:178, from /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: /home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71: note: parameter passing for argument of type ‘gnu_cxx::__normal_iterator<const double*, std::vector >’ changed in GCC 7.1 return primitive_range_wrapimpl__nocast<InputIterator,T>(first, last, typename std::iterator_traits::iterator_category());

In file included from /usr/include/c++/8/vector:64,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘Rcpp::DataFrame
RcppPwiz::getChromatogramsInfo(int)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for
argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double>
>’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for
argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double>
>’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:178,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
             return
primitive_range_wrap__impl__nocast<InputIterator,T>(first, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
             return
primitive_range_wrap__impl__nocast<InputIterator,T>(first, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c RcppPwizModule.cpp -o
RcppPwizModule.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c RcppIdent.cpp -o RcppIdent.o
In file included from /usr/include/c++/8/vector:69,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void
std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp,
_Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp =
double; _Alloc = std::allocator<double>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for
argument of type ‘std::vector<double>::iterator’ {aka
‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’} changed in
GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:178,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:
In function ‘SEXPREC*
Rcpp::internal::primitive_range_wrap__impl__nocast(InputIterator,
InputIterator, std::random_access_iterator_tag) [with InputIterator =
__gnu_cxx::__normal_iterator<const double*, std::vector<double> >; T =
double]’:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:112:21:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
         inline SEXP primitive_range_wrap__impl__nocast(InputIterator
first, InputIterator last,
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:112:21:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:112:21:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:
In member function ‘Rcpp::DataFrame RcppIdent::getScore()’:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
             return
primitive_range_wrap__impl__nocast<InputIterator,T>(first, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘Rcpp::DataFrame
RcppIdent::getModInfo()’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for
argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double>
>’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:178,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
             return
primitive_range_wrap__impl__nocast<InputIterator,T>(first, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:
In static member function ‘static Rcpp::Vector<RTYPE, StoragePolicy>
Rcpp::Vector<RTYPE,
StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const
T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&,
const T9&, const T10&, const T11&, const T12&, const T13&, const T14&,
const T15&, const T16&, const T17&, const T18&) [with T1 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T2 = Rcpp::traits::named_object<std::vector<int> >; T3 =
Rcpp::traits::named_object<std::vector<int> >; T4 =
Rcpp::traits::named_object<std::vector<bool> >; T5 =
Rcpp::traits::named_object<std::vector<double> >; T6 =
Rcpp::traits::named_object<std::vector<double> >; T7 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T8 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T9 = Rcpp::traits::named_object<std::vector<int> >; T10 =
Rcpp::traits::named_object<std::vector<bool> >; T11 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T12 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T13 = Rcpp::traits::named_object<std::vector<int> >; T14 =
Rcpp::traits::named_object<std::vector<int> >; T15 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T16 = Rcpp::traits::named_object<std::vector<int> >; T17 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; T18 =
Rcpp::traits::named_object<std::vector<std::__cxx11::basic_string<char> >
>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’:
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
irst, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp/internal/wrap.h:167:71:
note: parameter passing for argument of type
‘__gnu_cxx::__normal_iterator<const double*, std::vector<double> >’ changed
in GCC 7.1
             return
primitive_range_wrap__impl__nocast<InputIterator,T>(first, last, typename
std::iterator_traits<InputIterator>::iterator_category());

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/RcppCommon.h:59,
                 from
/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘Rcpp::DataFrame
RcppIdent::getPsmInfo()’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for
argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double>
>’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for
argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double>
>’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c RcppIdentModule.cpp -o
RcppIdentModule.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/regex/src/fileiter.cpp
-o boost/libs/regex/src/fileiter.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/regex/src/cregex.cpp -o
boost/libs/regex/src/cregex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/regex/src/instances.cpp
-o boost/libs/regex/src/instances.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/regex/src/regex.cpp -o
boost/libs/regex/src/regex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c
boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/iostreams/src/zlib.cpp
-o boost/libs/iostreams/src/zlib.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c
boost/libs/filesystem/src/operations.cpp -o
boost/libs/filesystem/src/operations.o
boost/libs/filesystem/src/operations.cpp: In function ‘int
{anonymous}::readdir_r_simulator(DIR*, dirent*, dirent**)’:
boost/libs/filesystem/src/operations.cpp:2094:18: warning: ‘int
readdir_r(DIR*, dirent*, dirent**)’ is deprecated
[-Wdeprecated-declarations]
       { return ::readdir_r(dirp, entry, result); }
                  ^~~~~~~~~
In file included from /usr/include/features.h:424,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/os_defines.h:39,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/c++config.h:508,
                 from /usr/include/c++/8/cstddef:49,
                 from ./boost/boost/config/compiler/gcc.hpp:165,
                 from ./boost/boost/config.hpp:39,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/dirent.h:189:12: note: declared here
 extern int __REDIRECT (readdir_r,
            ^~~~~~~~~~
boost/libs/filesystem/src/operations.cpp:2094:47: warning: ‘int
readdir_r(DIR*, dirent*, dirent**)’ is deprecated
[-Wdeprecated-declarations]
       { return ::readdir_r(dirp, entry, result); }
                                               ^
In file included from /usr/include/features.h:424,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/os_defines.h:39,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/c++config.h:508,
                 from /usr/include/c++/8/cstddef:49,
                 from ./boost/boost/config/compiler/gcc.hpp:165,
                 from ./boost/boost/config.hpp:39,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/dirent.h:189:12: note: declared here
 extern int __REDIRECT (readdir_r,
            ^~~~~~~~~~
boost/libs/filesystem/src/operations.cpp:2094:47: warning: ‘int
readdir_r(DIR*, dirent*, dirent**)’ is deprecated
[-Wdeprecated-declarations]
       { return ::readdir_r(dirp, entry, result); }
                                               ^
In file included from /usr/include/features.h:424,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/os_defines.h:39,
                 from
/usr/include/arm-linux-gnueabihf/c++/8/bits/c++config.h:508,
tddef:49,        from /usr/include/c++/8/cs
                 from ./boost/boost/config/compiler/gcc.hpp:165,
                 from ./boost/boost/config.hpp:39,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
/usr/include/dirent.h:189:12: note: declared here
 extern int __REDIRECT (readdir_r,
            ^~~~~~~~~~
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rhdf5lib/include'
-I/usr/local/include   -fpic  -g -O2  -c boost/libs/filesystem/src/path.cpp
-o boost/libs/filesystem/src/path.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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"/usr/local/lib/R/include" -DNDEBUG -I./boost_aux/
-I./boost/ -I. -I./pwiz/data/msdata/ramp/ -D_LARGEFILE_SOURCE
-DHAVE_PWIZ_MZML_LIB -D_NODEBUG
 -I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/Rcpp/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/zlibbioc/include'
-I'/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/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
make: *** No rule to make target 'pwiz/data/msdata/Version.o', needed by
'mzR.so'.  Stop.
ERROR: compilation failed for package ‘mzR’
* removing ‘/home/pi/R/armv7l-unknown-linux-gnueabihf-library/4.0/mzR’
Error in (function (command = NULL, args = character(), error_on_status =
TRUE,  :
  System command 'R' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occured
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: armv7l-unknown-linux-gnueabihf (32-bit)
Running under: Raspbian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] devtools_2.3.2 usethis_2.0.0

loaded via a namespace (and not attached):
 [1] magrittr_2.0.1    pkgload_1.1.0     R6_2.5.0          rlang_0.4.9
 [5] fansi_0.4.1       tools_4.0.3       pkgbuild_1.2.0    sessioninfo_1.1.1
 [9] cli_2.2.0         withr_2.3.0       ellipsis_0.3.1    remotes_2.2.0
[13] assertthat_0.2.1  digest_0.6.27     rprojroot_2.0.2   lifecycle_0.2.0
[17] crayon_1.3.4      processx_3.4.5    purrr_0.3.4       callr_3.5.1
[21] fs_1.5.0          ps_1.5.0          testthat_3.0.1    memoise_1.1.0
[25] glue_1.4.2        compiler_4.0.3    desc_1.2.0        prettyunits_1.1.1
>

On Thu, 10 Dec 2020 at 10:32, Steffen Neumann <notifications@github.com>
wrote:

> Hi, so it seems this is indeed a C++ compiler error:
>
> g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rcpp/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/zlibbioc/include" -I"/home/pi/R/arm-unknown-linux-gnueabihf-library/3.5/Rhdf5lib/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o
>
> ...
>
> ./boost/boost/smart_ptr/detail/shared_count.hpp:130:19: error: invalid new-expression of abstract class type ‘boost::detail::sp_counted_impl_p<boost::filesystem::detail::dir_itr_imp>’
>
> ...
>
> make: *** [/usr/lib/R/etc/Makeconf:171: RcppPwiz.o] Error 1
>
>
> I don't have an immediate solution. If possible, can you try to compile
> the branch with the new boost/pwiz in
> https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_20290 ?
> I didn't merge that branch yet, as it SEGV when reading the data, but it
> would be interesting
> to know if that at least compiles for you.
>
> Yours,
> Steffen
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/sneumann/mzR/issues/235#issuecomment-742433812>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ADK7OQO23QEJUTXV53HJSVTSUCPU7ANCNFSM4TTKDQGA>
> .
>

[sneumann]

Hi @adelomana , does mzR >= 2.29.3 work now on the Pi ? If yes, please report back so we can close this issue. Yours, Steffen P.S.: Happy Pi-Day :-)

[adelomana]

oh, sorry for the late reply Steffen.

I tried to fix the error but I never managed to do so. Unfortunately, I gave up and moved forward to another machine. Working on the Raspberry was just for fun. But yeah, please close the issue.

Thanks a lot for checking on this.

Best regards.

On Mon, 14 Mar 2022 at 15:15, Steffen Neumann @.***> wrote:

Hi @adelomana https://github.com/adelomana , does mzR >= 2.29.3 work now on the Pi ? If yes, please report back so we can close this issue. Yours, Steffen P.S.: Happy Pi-Day :-)

— Reply to this email directly, view it on GitHub https://github.com/sneumann/mzR/issues/235#issuecomment-1066926826, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADK7OQIDPZ54VRPY3VHXL73U75JZBANCNFSM4TTKDQGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[sneumann]

Indeed, that can be fun like the good text adventures from old times! Yours, Steffen