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uni-halle / gerbil

A fast and memory-efficient k-mer counter with GPU-support
MIT License
34 stars 14 forks source link

cmake and make error #19

Closed mewu3 closed 3 years ago

mewu3 commented 3 years ago

I have been trying to install gerbil on lab server, required libraries are installed.

cmake log: 

-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found version "1.71.0") found components: system thread filesystem regex 
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found Threads: TRUE  
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) 
-- Build type: Release
-- Configuring done
-- Generating done
-- Build files have been written to: /path/../../lib/gerbil/build

and make log: 

Scanning dependencies of target toFasta
[  5%] Building CXX object CMakeFiles/toFasta.dir/src/gerbil/toFasta.cpp.o
[ 11%] Linking CXX executable toFasta
[ 11%] Built target toFasta
Scanning dependencies of target gerbil
[ 17%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o
[ 23%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Bundle.cpp.o
[ 29%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastFile.cpp.o
[ 35%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastParser.cpp.o
[ 41%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastReader.cpp.o
[ 47%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/KmcWriter.cpp.o
[ 52%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/KmerDistributor.cpp.o
[ 58%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SequenceSplitter.cpp.o
[ 64%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SuperReader.cpp.o
[ 70%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SuperWriter.cpp.o
[ 76%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/TempFile.cpp.o
[ 82%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/debug.cpp.o
[ 88%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/gerbil.cpp.o
[ 94%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/global.cpp.o
[100%] Linking CXX executable gerbil
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x26): undefined reference to `boost::re_detail_107200::put_mem_block(void*)'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `void boost::re_detail_107200::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
Application.cpp:(.text._ZN5boost16re_detail_10720011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10720011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_107200::raise_runtime_error(std::runtime_error const&)'
/usr/bin/ld: Application.cpp:(.text._ZN5boost16re_detail_10720011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10720011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xf1): undefined reference to `boost::re_detail_107200::get_default_error_string(boost::regex_constants::error_type)'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_then()':
Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE10match_thenEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE10match_thenEv]+0x72): undefined reference to `boost::re_detail_107200::get_mem_block()'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_toggle_case()':
Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE17match_toggle_caseEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE17match_toggle_caseEv]+0x8a): undefined reference to `boost::re_detail_107200::get_mem_block()'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x1c): undefined reference to `boost::re_detail_107200::get_mem_block()'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_107200::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_107200::re_set_long<unsigned int> const*, boost::re_detail_107200::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
Application.cpp:(.text._ZN5boost16re_detail_10720016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10720016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x43f): undefined reference to `boost::re_detail_107200::cpp_regex_traits_implementation<char>::transform_primary[abi:cxx11](char const*, char const*) const'
/usr/bin/ld: Application.cpp:(.text._ZN5boost16re_detail_10720016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10720016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x548): undefined reference to `boost::re_detail_107200::cpp_regex_traits_implementation<char>::transform[abi:cxx11](char const*, char const*) const'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_imp()':
Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv]+0x22): undefined reference to `boost::re_detail_107200::get_mem_block()'
/usr/bin/ld: Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv]+0x1b5): undefined reference to `boost::re_detail_107200::verify_options(unsigned int, boost::regex_constants::_match_flags)'
/usr/bin/ld: Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv]+0x265): undefined reference to `boost::re_detail_107200::put_mem_block(void*)'
/usr/bin/ld: Application.cpp:(.text._ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv[_ZN5boost16re_detail_10720012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9match_impEv]+0x671): undefined reference to `boost::re_detail_107200::put_mem_block(void*)'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o: in function `bool boost::regex_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)':
Application.cpp:(.text._ZN5boost11regex_matchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsE[_ZN5boost11regex_matchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsE]+0x105): undefined reference to `boost::re_detail_107200::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, 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)'
/usr/bin/ld: CMakeFiles/gerbil.dir/src/gerbil/FastReader.cpp.o: in function `gerbil::FastReader::FastReader(unsigned int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned char&)':
FastReader.cpp:(.text+0x122f): undefined reference to `boost::filesystem::detail::directory_iterator_construct(boost::filesystem::directory_iterator&, boost::filesystem::path const&, unsigned int, boost::system::error_code*)'
/usr/bin/ld: FastReader.cpp:(.text+0x1261): undefined reference to `boost::filesystem::directory_entry::get_status(boost::system::error_code*) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/gerbil.dir/build.make:305: gerbil] Error 1
make[1]: *** [CMakeFiles/Makefile2:124: CMakeFiles/gerbil.dir/all] Error 2
make: *** [Makefile:149: all] Error 2
srechner commented 3 years ago

It seems that your compiler has problems finding boost. Which operation system do you use? Maybe removing and re-installing boost will fix the problem?

mewu3 commented 3 years ago

thank you for your reply, I will see whether this would solve the problem.