Unable to compile without errors

[MaestSi]

Dear paragraph developers,
I am trying to compile paragraph on Ubuntu 14.04 using g++ 7.3.0 and cmake 3.14.0.
When I run:

cd /mnt/cifs01/simone/software/paragraph-build
/mnt/cifs01/simone/software/cmake-3.14.0/bin/cmake ../paragraph
make

I get error message:

[ 22%] Building CXX object src/c++/lib/CMakeFiles/grmpy_common.dir/grm/GraphAligner.cpp.o
In file included from /home/simone/home_disk/software/paragraph/external/gssw/gssw.h:19:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grm/GraphAligner.cpp:30:
/usr/lib/gcc/x86_64-linux-gnu/4.8/include/smmintrin.h:31:3: error: #error "SSE4.1 instruction set not enabled"
 # error "SSE4.1 instruction set not enabled"
   ^
In file included from /home/simone/home_disk/software/paragraph/src/c++/lib/grm/GraphAligner.cpp:30:0:
/home/simone/home_disk/software/paragraph/external/gssw/gssw.h:67:5: error: ‘__m128i’ does not name a type
     __m128i* pvE;
     ^
/home/simone/home_disk/software/paragraph/external/gssw/gssw.h:68:5: error: ‘__m128i’ does not name a type
     __m128i* pvHStore;
     ^
/home/simone/home_disk/software/paragraph/external/gssw/gssw.h:138:2: error: ‘__m128i’ does not name a type
  __m128i* profile_byte; // 0: none
  ^
/home/simone/home_disk/software/paragraph/external/gssw/gssw.h:140:2: error: ‘__m128i’ does not name a type
  __m128i* profile_word; // 0: none
  ^
make[2]: *** [src/c++/lib/CMakeFiles/grmpy_common.dir/build.make:414: src/c++/lib/CMakeFiles/grmpy_common.dir/grm/GraphAligner.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:486: src/c++/lib/CMakeFiles/grmpy_common.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

I saw a post on Github (vgteam/vg#99) where a similar error was solved setting CXXFLAGS environment variable, so I tried it out.

export CXXFLAGS=-msse4.1
/mnt/cifs01/simone/software/cmake-3.14.0/bin/cmake ../paragraph
make

That error seems to be partially solved, but then it stops again:

[ 26%] Building CXX object src/c++/lib/CMakeFiles/grmpy_common.dir/grmpy/AlignSamples.cpp.o
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp: In function ‘void grmpy::writeAlignments(Json::Value&, const grmpy::Parameters&, const paragraph::Parameters&, const string&, genotyping::SampleInfo&)’:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:76:105: error: no matching function for call to ‘regex_replace(const string&, const regex&, const char [2])’
     const std::string safe_sample_name = std::regex_replace(sample.sample_name(), unsafe_characters, "_");
                                                                                                         ^
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:76:105: note: candidates are:
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:76:105: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
     const std::string safe_sample_name = std::regex_replace(sample.sample_name(), unsafe_characters, "_");
                                                                                                         ^
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:76:105: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [2]’
     const std::string safe_sample_name = std::regex_replace(sample.sample_name(), unsafe_characters, "_");
                                                                                                         ^
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:82:31: error: no matching function for call to ‘regex_replace(boost::iterators::iterator_value<boost::iterators::transform_iterator<boost::range_detail::default_constructible_unary_fn_wrapper<grmpy::writeAlignments(Json::Value&, const grmpy::Parameters&, const paragraph::Parameters&, const string&, genotyping::SampleInfo&)::__lambda3, std::basic_string<char> >, std::_List_const_iterator<common::Region>, boost::iterators::use_default, boost::iterators::use_default> >::type, const regex&, const char [2])’
         unsafe_characters, "_");
                               ^
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:82:31: note: candidates are:
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:82:31: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
         unsafe_characters, "_");
                               ^
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:82:31: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [2]’
         unsafe_characters, "_");
                               ^
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:99:90: error: no matching function for call to ‘regex_replace(std::string&, const regex&, const char [2])’
     const std::string safe_graph_id = std::regex_replace(graph_id, unsafe_characters, "_");
                                                                                          ^
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:99:90: note: candidates are:
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:99:90: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
     const std::string safe_graph_id = std::regex_replace(graph_id, unsafe_characters, "_");
                                                                                          ^
In file included from /usr/include/c++/4.8/regex:62:0,
                 from /home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:49:
/usr/include/c++/4.8/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
/home/simone/home_disk/software/paragraph/src/c++/lib/grmpy/AlignSamples.cpp:99:90: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [2]’
     const std::string safe_graph_id = std::regex_replace(graph_id, unsafe_characters, "_");
                                                                                          ^
make[2]: *** [src/c++/lib/CMakeFiles/grmpy_common.dir/build.make:492: src/c++/lib/CMakeFiles/grmpy_common.dir/grmpy/AlignSamples.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:486: src/c++/lib/CMakeFiles/grmpy_common.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

I know Ubuntu 14.04 is not amongst the distributions you have tested paragraph on.
Do you have any ideas about how I could solve it? Thanks.
Simone

[pkrusche]

Are you sure the correct version of g++ is being used? From the include paths in the errors it looks like the compiler being used is g++ 4.8. The right compiler version can be set using update-alternatives in Ubuntu: https://stackoverflow.com/questions/7832892/how-to-change-the-default-gcc-compiler-in-ubuntu (or using the CXX environment variable before running cmake, also it is important to reset the CMake cache / empty the build folder after changing this).

[MaestSi]

You were right, I was using the old g++ version; I thought it was enough to have the new one in the PATH environment variable before the other version, and that when performing which g++ I had the correct version, but that is not true.
So, I set:
export CXX=/mnt/cifs01/simone/software/gcc-7.3.0/bin/g++
and I emptied the build folder; I had already exported the Boost library with:
export BOOST_ROOT=/mnt/cifs01/simone/software/boost_1_58_0/
However, another error occurs:

[ 66%] Linking CXX executable ../../../bin/paragraph
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_st ring<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)': paragraph.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5E NS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x32): undefined reference to boost::program_options::validation_error::get_template[abi:cxx11](boost::program_op
tions::validation_error::kind_t)'
paragraph.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x4f): undefined reference to boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)' CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const':
paragraph.cpp:(.text._ZNK5boost15program_options13variables_mapixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK5boost15program_options13variables_mapixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x1f): undefined reference to boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<float, char>::name[abi:cxx11]() const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIfcE4nameB5cxx11Ev]+0x32): undefined reference to boost::program_options::arg[abi:cxx11]'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<int, char>::name[abi:cxx11]() const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIicE4nameB5cxx11Ev]+0x32): undefined reference to boost::program_options::arg[abi:cxx11]'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<bool, char>::name[abi:cxx11]() const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIbcE4nameB5cxx11Ev]+0x32): undefined reference to boost::program_options::arg[abi:cxx11]'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x7a): undefined reference to boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool*, int)'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x32): undefined reference to boost::program_options::arg[abi:cxx11]'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x7a): undefined reference to boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int)'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const': paragraph.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x32): undefined reference to boost::program_options::arg[abi:cxx11]'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long)': paragraph.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0xfe): undefined reference to boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)': paragraph.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0xfa): undefined reference to boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
CMakeFiles/paragraph.dir/paragraph.cpp.o: In function void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)': paragraph.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x160): undefined reference to boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int)'
paragraph.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x267): undefined reference to boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
CMakeFiles/paragraph.dir/paragraph.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' ../../../lib/libgrm.a(Program.cpp.o): In function common::Options::parse(char const*, int, char const* const*)':
Program.cpp:(.text+0x1a51): undefined reference to boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' ../../../lib/libgrm.a(Program.cpp.o): In function common::compareOptionName(boost::shared_ptrboost::program_options::option_description const&, boost::shared_ptrboost::program_options::option_description const&)':
Program.cpp:(.text+0x2c31): undefined reference to boost::program_options::option_description::long_name[abi:cxx11]() const' Program.cpp:(.text+0x2c48): undefined reference to boost::program_options::option_description::long_nameabi:cxx11 const'
../../../lib/libgrm.a(Program.cpp.o): In function common::Options::helpDefaults[abi:cxx11](std::vector<boost::shared_ptr<boost::program_options::option_description>, std::allocator<boost::shared_ptr<boost::program_options::option_description> > > const&) const': Program.cpp:(.text+0x2dda): undefined reference to boost::program_options::option_description::format_parameterabi:cxx11 const'
Program.cpp:(.text+0x2dee): undefined reference to boost::program_options::option_description::long_name[abi:cxx11]() const' ../../../lib/libgrm.a(Program.cpp.o): In function common::Options::help[abi:cxx11](std::vector<boost::shared_ptrboost::program_options::option_description, std::allocator<boost::shared_ptrboost::program_options::option_description > > const&, bool) const':
Program.cpp:(.text+0x30b2): undefined reference to boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' ../../../lib/libgrm.a(Program.cpp.o): In function boost::program_options::error_with_option_name::get_option_nameabi:cxx11 const':
Program.cpp:(.text._ZNK5boost15program_options22error_with_option_name15get_option_nameB5cxx11Ev[_ZNK5boost15program_options22error_with_option_name15get_option_nameB5cxx11Ev]+0x1f): undefined reference to boost::program_options::error_with_option_name::get_canonical_option_name[abi:cxx11]() const' ../../../lib/libgrm.a(Program.cpp.o): In function boost::program_options::basic_command_line_parser::basic_command_line_parser(int, char const* const*)':
Program.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x72): undefined reference to boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' ../../../lib/libgrm.a(Program.cpp.o): In function boost::program_options::basic_command_line_parser::basic_command_line_parser(std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&)':
Program.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2ERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EE[_ZN5boost15program_options25basic_command_line_parserIcEC5ERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EE]+0x33): undefined reference to boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' ../../../lib/libgrm.a(Program.cpp.o): In function std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > boost::program_options::to_internal<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >(std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&)':
Program.cpp:(.text._ZN5boost15program_options11to_internalINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIS7_SaIS7_EERKS8_IT_SaISB_EE[_ZN5boost15program_options11to_internalINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIS7_SaIS7_EERKS8_IT_SaISB_EE]+0x5d): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [src/c++/main/CMakeFiles/paragraph.dir/build.make:95: bin/paragraph] Error 1
make[1]: *** [CMakeFiles/Makefile2:607: src/c++/main/CMakeFiles/paragraph.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

Any other suggestions?
Thanks

[pkrusche]

If you compiled Boost with the old compiler version then you will need to rebuild it with gcc 7 and use that one. Gcc 4 and 7 are not compatible when it comes to linking (see https://github.com/Illumina/paragraph#library-dependencies for some help on building Boost).

[MaestSi]

Thank you again, there was a problem in my Boost library. When using the embedded one with -DUSE_SYSTEM_BOOST=FALSE all went smoothly.
Simone

[MaestSi]

Maybe not a consequence of compilation errors (I didn't get any), but while when I run ./bin/paragraph -h the help message is printed out, when I try the example instruction I get some errors.
In particular, the command is:
python3 ./bin/multigrmpy.py -i share/test-data/round-trip-genotyping/candidates.json -m share/test-data/round-trip-genotyping/samples.txt -r share/test-data/round-trip-genotyping/dummy.fa -o ./test
And the error is:

File "./bin/multigrmpy.py", line 302
raise Exception(f"Cannot create alignment output directory: {alignment_directory}")
^
SyntaxError: invalid syntax

I also tried with absolute path but nothing changed.
Thanks,

[MaestSi]

I tried with another python version (the previous one was 3.4.3). I had to pip install intervaltree module on the newer python version, but now everything works.
Thanks again.