Make error

[gbdias]

Hi @AlexanderDilthey,

I'm running into some installation problems that were discussed in other issues (https://github.com/DiltheyLab/MetaMaps/issues/20), but the solutions mentioned before don't seem to be working for me.

• I used a conda environment with all dependencies and I get the make error collect2: error: ld returned 1 exit status

• Here are the steps I followed:

  conda create -n metamaps -c conda-forge autoconf boost zlib icu==64.2
  conda activate metamaps
  conda install -c anaconda gcc
  git clone https://github.com/DiltheyLab/MetaMaps
  cd MetaMaps
  ./bootstrap.sh
  ./configure --with-boost=$CONDA_PREFIX --prefix=$CONDA_PREFIX
  LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
  make

• And here is the make error message:

(metamaps2) gd98309@sapelo2-sub1 MetaMaps$ make
g++ -c -O2 -ggdb -fopenmp -std=c++11 -Isrc -L /home/gd98309/miniconda/envs/metamaps2/lib -I /home/gd98309/miniconda/envs/metamaps2/include  -include src/common/memcpyLink.h -Wl,--wrap=memcpy -DUSE_BOOST -o src/map/mash_map.o src/map/mash_map.cpp
g++ -O2 -ggdb -fopenmp -std=c++11 -Isrc -L /home/gd98309/miniconda/envs/metamaps2/lib -I /home/gd98309/miniconda/envs/metamaps2/include  -include src/common/memcpyLink.h -Wl,--wrap=memcpy -DUSE_BOOST src/map/mash_map.o   -o metamaps /home/gd98309/miniconda/envs/metamaps2/lib/libboost_math_c99.a -lstdc++ -fopenmp -lz -lm -lpthread -lboost_system -lboost_filesystem -lboost_serialization -lboost_regex
/usr/bin/ld: warning: libicudata.so.64, needed by /home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libicui18n.so.64, needed by /home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libicuuc.so.64, needed by /home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so, not found (try using -rpath or -rpath-link)
src/map/mash_map.o: In function `save_primitive<boost::archive::text_oarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::string const&)'
src/map/mash_map.o: In function `save_primitive<boost::archive::binary_oarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits<char> >::save(std::string const&)'
src/map/mash_map.o: In function `perl_matcher':
/home/gd98309/miniconda/envs/metamaps2/include/boost/regex/v4/perl_matcher.hpp:391: undefined reference to `boost::re_detail_107000::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
src/map/mash_map.o: In function `boost::cpp_regex_traits<char>::transform_primary(char const*, char const*) const':
/home/gd98309/miniconda/envs/metamaps2/include/boost/regex/v4/cpp_regex_traits.hpp:966: undefined reference to `boost::re_detail_107000::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
src/map/mash_map.o: In function `boost::cpp_regex_traits<char>::transform(char const*, char const*) const':
/home/gd98309/miniconda/envs/metamaps2/include/boost/regex/v4/cpp_regex_traits.hpp:962: undefined reference to `boost::re_detail_107000::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
src/map/mash_map.o: In function `boost::re_detail_107000::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
/home/gd98309/miniconda/envs/metamaps2/include/boost/regex/v4/perl_matcher_common.hpp:346: undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > > const&)'
src/map/mash_map.o: In function `boost::re_detail_107000::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
/home/gd98309/miniconda/envs/metamaps2/include/boost/regex/v4/perl_matcher_non_recursive.hpp:1108: undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > > const&)'
src/map/mash_map.o: In function `save_primitive<boost::archive::text_oarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::string const&)'
src/map/mash_map.o: In function `load_primitive<boost::archive::text_iarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/iserializer.hpp:108: undefined reference to `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::string&)'
src/map/mash_map.o: In function `save_primitive<boost::archive::text_oarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::string const&)'
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::string const&)'
src/map/mash_map.o: In function `save_primitive<boost::archive::binary_oarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/oserializer.hpp:93: undefined reference to `boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits<char> >::save(std::string const&)'
src/map/mash_map.o: In function `load_primitive<boost::archive::binary_iarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/iserializer.hpp:108: undefined reference to `boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits<char> >::load(std::string&)'
src/map/mash_map.o: In function `load_primitive<boost::archive::text_iarchive, std::basic_string<char> >':
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/iserializer.hpp:108: undefined reference to `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::string&)'
/home/gd98309/miniconda/envs/metamaps2/include/boost/archive/detail/iserializer.hpp:108: undefined reference to `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::string&)'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::str() const@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::numpunct<wchar_t> const& std::use_facet<std::__cxx11::numpunct<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::collate<wchar_t> const& std::use_facet<std::__cxx11::collate<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `bool std::has_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `icu_64::Locale::~Locale()'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_charType_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::overflow_error::overflow_error(char const*)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `icu_64::Locale::Locale(icu_64::Locale const&)'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::_V2::error_category::~error_category()@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `bool std::has_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::_V2::error_category::_M_message[abi:cxx11](int) const@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::numpunct<char> const& std::use_facet<std::__cxx11::numpunct<char> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_isblank_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::logic_error::logic_error(char const*)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::invalid_argument::invalid_argument(char const*)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::messages<char> const& std::use_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `icu_64::Locale::Locale()'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_isspace_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `std::_V2::generic_category()@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_tolower_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `typeinfo for std::_V2::error_category@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_filesystem.so: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `icu_64::Collator::createInstance(icu_64::Locale const&, UErrorCode&)'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_digit_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `u_charFromName_64'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::collate<char> const& std::use_facet<std::__cxx11::collate<char> >(std::locale const&)@GLIBCXX_3.4.21'
/home/gd98309/miniconda/envs/metamaps2/lib/libboost_regex.so: undefined reference to `std::__cxx11::messages<wchar_t> const& std::use_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make: *** [metamaps] Error 1

[AlexanderDilthey]

Hi @gbdias, I would recommend using a system or custom installation of boost.