Install fails on Ubuntu 16.04

[linsalrob]

Install of both version 2.22 and 2.23 (64 bit) does not install:

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 toboost::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 functionboost::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 functionvoid CHitUnit::serializeboost::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 toboost::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 toboost::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 functionboost::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 toboost::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 toboost::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/

[zhaoyanswill]

It seems the library path is not correct. Where are the boost libraries? Thanks!

[linsalrob]

I have the libraries in the 2.23/Src directory I downloaded from sourceforge

$ ls Src/
aa.h           BlastStat.h  BuildHash.cpp  codon.h         HashSearch.h  libboost_chrono.a         libboost_system.a  lnfac.h   Makefile       mergeUnit.h  paras.h  Seg.h       threadpool.hpp
BlastStat.cpp  boost        cindex.h       HashSearch.cpp  hitUnit.h     libboost_serialization.a  libboost_thread.a  main.cpp  mergeUnit.cpp  n2a.h        Seg.cpp  threadpool  weight.h

and I also have boost installed:

/usr/lib/x86_64-linux-gnu/libboost_date_time.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_filesystem.a
/usr/lib/x86_64-linux-gnu/libboost_filesystem.so
/usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_regex.a
/usr/lib/x86_64-linux-gnu/libboost_regex.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_system.a
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0
/usr/lib/x86_64-linux-gnu/libboost_thread.so.1.58.0

that is in my LD_LINKER_PATH too

Rob

[zhaoyanswill]

What's 'LIB' in Makefile? Thanks!

[linsalrob]

LIBS := -L ./

[zhaoyanswill]

Please try -L /usr/lib/x86_64-linux-gnu/

[linsalrob]

The problem is that Ubuntu is using gcc-5 (my machine has version 5.4.0) and the boost libs do not compile with that version.

The solution is to edit the Makefile in Src and change the line

CXX := g++

to

CXX := g++-4.8

All my Ubuntu systems include a version of gcc-4.x, but you should confirm the version that you have, e.g. by typing g++ and pressing two tabs on the command line.

With this change the code compiles and installs.

[pcantalupo]

Same thing happened to me. Thank you @linsalrob for the fix