Can't install mzR on Ubuntu 20.04

OmarLaham commented 3 years ago
Hi, I'm trying to isntall mzR on Ubuntu 20.04 but I get the following messages. (Bioconductor version: 3.12, R version > 4).
> * installing *source* package ‘mzR’ ...
** using staged installation
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o 
find . -name \*~ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/zlibbioc/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -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/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/zlibbioc/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -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/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/zlibbioc/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -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]
  395 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  242 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  441 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  454 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  520 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  529 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
  531 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:52,
                 from /home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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/omar/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/zlibbioc/include' -I'/home/omar/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppRamp.cpp -o RcppRamp.o
make: *** [/usr/lib/R/etc/Makeconf:181: RcppRamp.o] Interrupt
Thanks!
OmarLaham commented 3 years ago
gcc --version -> gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
lgatto commented 3 years ago
It just says interrupt, but mentions no error. I have no issues with the same setup. Are you sure something else didn't trigger the interruption? Also, what command did you use?
OmarLaham commented 3 years ago
I interrupted it because it goes in endless execution with some errors or maybe warning like:
template class auto_ptr; | ^~~~
OmarLaham commented 3 years ago
You are right. that's a warning not an error. I will give it more time and post back. Thanks
lgatto commented 3 years ago
You need to be patient, mzR does take time to compile.
sneumann / mzR

Can't install mzR on Ubuntu 20.04 #242
