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Failed install on Ubuntu 18.0 LTS #44

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xiaole99 opened this issue Oct 3, 2018 · 7 comments
Open

Failed install on Ubuntu 18.0 LTS #44

xiaole99 opened this issue Oct 3, 2018 · 7 comments

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@xiaole99
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xiaole99 commented Oct 3, 2018

When I installed after typing ./install, the error returned as below:

RAPSearch installer
rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
HashSearch.o: In function boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::vsave(boost::archive::class_name_type const&)': HashSearch.cpp:(.text._ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE[_ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE]+0x59): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
HashSearch.o: In function boost::archive::detail::oserializer<boost::archive::binary_oarchive, 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> > > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const': HashSearch.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xcb): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
HashSearch.o: In function boost::archive::detail::iserializer<boost::archive::binary_iarchive, 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> > > > >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const': HashSearch.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x11c): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
HashSearch.o: In function void CHitUnit::serialize<boost::archive::binary_oarchive>(boost::archive::binary_oarchive&, unsigned int)': HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x171): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x185): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits<char> >::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x19c): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1b3): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits<char> >::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1ce): undefined reference to boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
mergeUnit.o: In function boost::archive::detail::iserializer<boost::archive::binary_iarchive, CHitUnit>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const': mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x22f): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x23b): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits<char> >::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x24a): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x259): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits<char> >::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x268): undefined reference to boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
collect2: error: ld returned 1 exit status
Makefile:33: recipe for target 'rapsearch' failed
make: *** [rapsearch] Error 1
mv: cannot stat 'Src/rapsearch': No such file or directory
mv: cannot stat 'Src/prerapsearch': No such file or directory

Executables are now installed under bin/

Then I try to change the boost library to my /usr/lib/x86_64-linux-gnu/
by modifying "Makefile"
LIBS := -L /usr/lib/x86_64-linux-gnu/

There is still error like:

RAPSearch installer
rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L /usr/lib/x86_64-linux-gnu/ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
HashSearch.o: In function CHashSearch::Search(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, int, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, 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> > > >&)': HashSearch.cpp:(.text+0xd45d): undefined reference to boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
HashSearch.cpp:(.text+0xd4da): undefined reference to boost::archive::detail::shared_ptr_helper::shared_ptr_helper()' HashSearch.o: In function boost::archive::binary_iarchive::~binary_iarchive()':
HashSearch.cpp:(.text._ZN5boost7archive15binary_iarchiveD0Ev[_ZN5boost7archive15binary_iarchiveD5Ev]+0x16): undefined reference to boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()' HashSearch.o: In function boost::archive::binary_iarchive::~binary_iarchive()':
HashSearch.cpp:(.text._ZN5boost7archive15binary_iarchiveD2Ev[_ZN5boost7archive15binary_iarchiveD5Ev]+0x16): undefined reference to boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()' HashSearch.o: In function boost::threadpool::detail::pool_core<boost::function0, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks>::shutdown()':
HashSearch.cpp:(.text._ZN5boost10threadpool6detail9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEE8shutdownEv[_ZN5boost10threadpool6detail9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEE8shutdownEv]+0x116): undefined reference to boost::thread::join()' HashSearch.o: In function boost::threadpool::detail::worker_thread<boost::threadpool::detail::pool_core<boost::function0, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> >::create_and_attach(boost::shared_ptr<boost::threadpool::detail::pool_core<boost::function0, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> > const&)':
HashSearch.cpp:(.text._ZN5boost10threadpool6detail13worker_threadINS1_9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEEEE17create_and_attachERKNS_10shared_ptrISA_EE[_ZN5boost10threadpool6detail13worker_threadINS1_9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEEEE17create_and_attachERKNS_10shared_ptrISA_EE]+0x33f): undefined reference to boost::thread::start_thread()' mergeUnit.o: In function CMergeUnit::CMergeUnit(char const)':
mergeUnit.cpp:(.text+0x3b6): undefined reference to boost::archive::detail::shared_ptr_helper::shared_ptr_helper()' mergeUnit.cpp:(.text+0x418): undefined reference to boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
mergeUnit.o: In function CMergeUnit::Update(int, std::vector<CHitUnit, std::allocator<CHitUnit> >&)': mergeUnit.cpp:(.text+0x980): undefined reference to boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
mergeUnit.cpp:(.text+0xac3): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
collect2: error: ld returned 1 exit status
Makefile:33: recipe for target 'rapsearch' failed
make: *** [rapsearch] Error 1
mv: cannot stat 'Src/rapsearch': No such file or directory
mv: cannot stat 'Src/prerapsearch': No such file or directory

Executables are now installed under bin/
@MarcoT800
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same error in Ubuntu 17.04 under Virtual Machine

RAPSearch installer
rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
/usr/bin/ld: .//libboost_serialization.a(basic_iarchive.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail14basic_iarchiveE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_iserializer.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail17basic_iserializerE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(basic_oarchive.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail14basic_oarchiveE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_oserializer.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail17basic_oserializerE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(binary_iarchive.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(binary_oarchive.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(extended_type_info.o): relocation R_X86_64_32S against symbol _ZTVN5boost13serialization18extended_type_infoE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(extended_type_info_typeid.o): relocation R_X86_64_32S against symbol _ZTVN5boost13serialization13typeid_system27extended_type_info_typeid_0E' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(archive_exception.o): relocation R_X86_64_32S against symbol _ZNSs4_Rep20_S_empty_rep_storageE@@GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(shared_ptr_helper.o): relocation R_X86_64_32S against symbol _ZTVN5boost6detail18sp_counted_impl_pdIPKvNS_7archive6detail17shared_ptr_helper12null_deleterEEE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(basic_archive.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_serializer_map.o): relocation R_X86_64_32 against symbol __gxx_personality_v0@@CXXABI_1.3' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_serialization.a(void_cast.o): relocation R_X86_64_32 against symbol _ZZN5boost13serialization9singletonISt3setIPKNS0_16void_cast_detail11void_casterENS3_19void_caster_compareESaIS6_EEE12get_instanceEvE1t' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_thread.a(thread.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: .//libboost_thread.a(once.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_system.a(error_code.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
HashSearch.o: nella funzione "boost::archive::detail::common_oarchiveboost::archive::binary_oarchive::vsave(boost::archive::class_name_type const&)":
HashSearch.cpp:(.text._ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE[_ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE]+0x5d): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.o: nella funzione "boost::archive::detail::oserializer<boost::archive::binary_oarchive, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const) const":
HashSearch.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xd3): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.o: nella funzione "boost::archive::detail::iserializer<boost::archive::binary_iarchive, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const":
HashSearch.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x152): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
HashSearch.o: nella funzione "void CHitUnit::serializeboost::archive::binary_oarchive(boost::archive::binary_oarchive&, unsigned int)":
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x171): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x185): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x19c): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1b3): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1ce): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
mergeUnit.o: nella funzione "boost::archive::detail::iserializer<boost::archive::binary_iarchive, CHitUnit>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const":
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x233): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x23f): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x24e): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x25d): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x26c): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
/usr/bin/ld: link finale non riuscito: Il simbolo richiede una sezione di debug che non esiste
collect2: error: ld returned 1 exit status
Makefile:33: set di istruzioni per l'obiettivo "rapsearch" non riuscito
make: *** [rapsearch] Errore 1
mv: impossibile eseguire stat di 'Src/rapsearch': File o directory non esistente
mv: impossibile eseguire stat di 'Src/prerapsearch': File o directory non esistente

Executables are now installed under bin/

@guangfazhang
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same error in Ubuntu 17.04 under Virtual Machine

RAPSearch installer
rm -f _.o rapsearch prerapsearch g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./ g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./ g++ -c -O3 -w Seg.cpp -o Seg.o -I ./ g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./ g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono /usr/bin/ld: .//libboost_serialization.a(basic_iarchive.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail14basic_iarchiveE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_iserializer.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail17basic_iserializerE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_oarchive.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail14basic_oarchiveE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_oserializer.o): relocation R_X86_64_32S against symbol _ZTVN5boost7archive6detail17basic_oserializerE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(binary_iarchive.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(binary_oarchive.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(extended_type_info.o): relocation R_X86_64_32S against symbol _ZTVN5boost13serialization18extended_type_infoE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(extended_type_info_typeid.o): relocation R_X86_64_32S against symbol _ZTVN5boost13serialization13typeid_system27extended_type_info_typeid_0E' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(archive_exception.o): relocation R_X86_64_32S against symbol _ZNSs4_Rep20_S_empty_rep_storageE@@GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(shared_ptr_helper.o): relocation R_X86_64_32S against symbol _ZTVN5boost6detail18sp_counted_impl_pdIPKvNS_7archive6detail17shared_ptr_helper12null_deleterEEE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_archive.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(basic_serializer_map.o): relocation R_X86_64_32 against symbol __gxx_personality_v0@@CXXABI_1.3' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_serialization.a(void_cast.o): relocation R_X86_64_32 against symbol _ZZN5boost13serialization9singletonISt3setIPKNS0_16void_cast_detail11void_casterENS3_19void_caster_compareESaIS6_EEE12get_instanceEvE1t' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_thread.a(thread.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_thread.a(once.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: .//libboost_system.a(error_code.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC HashSearch.o: nella funzione "boost::archive::detail::common_oarchiveboost::archive::binary_oarchive::vsave(boost::archive::class_name_type const&)": HashSearch.cpp:(.text._ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE[_ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE]+0x5d): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)" HashSearch.o: nella funzione "boost::archive::detail::oserializer<boost::archive::binary_oarchive, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::_cxx11::basic_string<char, std::char_traits, std::allocator > > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const) const":
HashSearch.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_15binary_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xd3): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.o: nella funzione "boost::archive::detail::iserializer<boost::archive::binary_iarchive, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const":
HashSearch.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x152): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
HashSearch.o: nella funzione "void CHitUnit::serializeboost::archive::binary_oarchive(boost::archive::binary_oarchive&, unsigned int)":
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x171): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x185): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x19c): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1b3): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
HashSearch.cpp:(.text._ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN8CHitUnit9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x1ce): riferimento non definito a "boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)"
mergeUnit.o: nella funzione "boost::archive::detail::iserializer<boost::archive::binary_iarchive, CHitUnit>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const":
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x233): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x23f): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x24e): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x25d): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
mergeUnit.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveE8CHitUnitE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x26c): riferimento non definito a "boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)"
/usr/bin/ld: link finale non riuscito: Il simbolo richiede una sezione di debug che non esiste
collect2: error: ld returned 1 exit status
Makefile:33: set di istruzioni per l'obiettivo "rapsearch" non riuscito
make: *** [rapsearch] Errore 1
mv: impossibile eseguire stat di 'Src/rapsearch': File o directory non esistente
mv: impossibile eseguire stat di 'Src/prerapsearch': File o directory non esistente

Executables are now installed under bin/

have you resovled this problem, i have met the same issue.

@MaryamZaheri
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I have the same problem on ubuntu 16.04, would you please let me know if there is a solution? I have tried g++-4.8 as well.

rm -f *.o rapsearch prerapsearch
g++-5 -c -O3 -w  HashSearch.cpp -o HashSearch.o -I /usr/include/boost -I ./
g++-5 -c -O3 -w  BlastStat.cpp -o BlastStat.o -I /usr/include/boost -I ./
g++-5 -c -O3 -w  Seg.cpp -o Seg.o -I /usr/include/boost -I ./
g++-5 -c -O3 -w  mergeUnit.cpp -o mergeUnit.o -I /usr/include/boost -I ./
g++-5 -O3 -w  -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I /usr/include/boost -I ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono -L /usr/lib/x86_64-linux-gnu/ -L ./
HashSearch.o: In function `CHashSearch::Search(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, int, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, 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> > > >&)':
HashSearch.cpp:(.text+0xd4dd): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
HashSearch.cpp:(.text+0xd55a): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
HashSearch.o: In function `boost::archive::binary_iarchive::~binary_iarchive()':
HashSearch.cpp:(.text._ZN5boost7archive15binary_iarchiveD0Ev[_ZN5boost7archive15binary_iarchiveD5Ev]+0x16): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
HashSearch.o: In function `boost::archive::binary_iarchive::~binary_iarchive()':
HashSearch.cpp:(.text._ZN5boost7archive15binary_iarchiveD2Ev[_ZN5boost7archive15binary_iarchiveD5Ev]+0x16): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
HashSearch.o: In function `boost::threadpool::detail::pool_core<boost::function0<void>, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks>::shutdown()':
HashSearch.cpp:(.text._ZN5boost10threadpool6detail9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEE8shutdownEv[_ZN5boost10threadpool6detail9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEE8shutdownEv]+0x116): undefined reference to `boost::thread::join()'
HashSearch.o: In function `boost::threadpool::detail::worker_thread<boost::threadpool::detail::pool_core<boost::function0<void>, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> >::create_and_attach(boost::shared_ptr<boost::threadpool::detail::pool_core<boost::function0<void>, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> > const&)':
HashSearch.cpp:(.text._ZN5boost10threadpool6detail13worker_threadINS1_9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEEEE17create_and_attachERKNS_10shared_ptrISA_EE[_ZN5boost10threadpool6detail13worker_threadINS1_9pool_coreINS_9function0IvEENS0_14fifo_schedulerENS0_11static_sizeENS0_17resize_controllerENS0_18wait_for_all_tasksEEEE17create_and_attachERKNS_10shared_ptrISA_EE]+0x33f): undefined reference to `boost::thread::start_thread()'
mergeUnit.o: In function `CMergeUnit::CMergeUnit(char const*)':
mergeUnit.cpp:(.text+0x3b6): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
mergeUnit.cpp:(.text+0x418): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
mergeUnit.o: In function `CMergeUnit::Update(int, std::vector<CHitUnit, std::allocator<CHitUnit> >&)':
mergeUnit.cpp:(.text+0x980): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'
mergeUnit.cpp:(.text+0xac3): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'
collect2: error: ld returned 1 exit status
make: *** [Makefile:33: rapsearch] Error 1
mv: cannot stat 'Src/rapsearch': No such file or directory
mv: cannot stat 'Src/prerapsearch': No such file or directory

Executables are now installed under bin/```

@MaryamZaheri MaryamZaheri mentioned this issue Dec 20, 2019
Closed
@stryke
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stryke commented Dec 20, 2019

We run rapsearch2 on Ubuntu 16.04. I can't guarantee anything, but here is the installation code:

# rapsearch
cd /usr/local/src
# 2.24 requires rebuilding the dbs
SRC="RAPSearch2.24_64bits"
curl -L -O "https://downloads.sourceforge.net/project/rapsearch2/${SRC}.tar.gz"
tar -zxf "${SRC}.tar.gz"
cd "${SRC}"
# rapsearch comes with boost libraries that are incompatible with installed g++
# current compiler will not compile
# current apt-get boost libraries caused a seg fault
# so use old compiler with rapsearch boost
apt-get install -y gcc-4.8 g++-4.8 g++-4.8-multilib gcc-4.8-multilib
CWD=`pwd`
cd Src/
cp Makefile Makefile.bak
sed 's/^CXX := g++$/&-4.8/' Makefile.bak > Makefile
cd ${CWD}
# now install rapsearch
./install
install bin/* /usr/local/bin

@MaryamZaheri
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Thank you very much, it worked.

@fatima267
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I am facing the same problem but I cannot install gcc 4.8

@ricardo-aaron
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to install g++-4.X follow these instructions:
https://askubuntu.com/questions/1036108/install-gcc-4-9-at-ubuntu-18-04

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@stryke @ricardo-aaron @MaryamZaheri @xiaole99 @MarcoT800 @guangfazhang @fatima267