compiling stript-it error. Please help me check which lib should be added and how to add the lib

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Zheng Zhao

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Nov 2, 2017, 5:18:48 PM11/2/17
to Silicos-it chemoinformatics
step 1: cmake
OpenBabel include directories: /home/localadm/source/openbabel-install/include
OpenBabel link library: /home/localadm/source/openbabel-install/lib/libopenbabel.so
Installation directory of executable: /home/localadm/source/strip-it-1.0.2/bin
-- Configuring done
-- Generating done
-- Build files have been written to: /home/localadm/source/strip-it-1.0.2
step 2: make
Scanning dependencies of target strip-it
[  4%] Building CXX object CMakeFiles/strip-it.dir/src/parseScaffoldDefinitions.cpp.o
[  9%] Building CXX object CMakeFiles/strip-it.dir/src/parseCommandLine.cpp.o
[ 13%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer.cpp.o
[ 18%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/murcko_2.cpp.o
[ 22%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/rings_with_linkers_1.cpp.o
[ 27%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/rings_with_linkers_2.cpp.o
[ 31%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer_5.cpp.o
[ 36%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/oprea_3.cpp.o
[ 40%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/oprea_2.cpp.o
[ 45%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/oprea.cpp.o
[ 50%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/oprea_1.cpp.o
[ 54%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/scaffold.cpp.o
[ 59%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer_4.cpp.o
[ 63%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer_1.cpp.o
[ 68%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer_2.cpp.o
[ 72%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/murcko_1.cpp.o
[ 77%] Building CXX object CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer_3.cpp.o
[ 81%] Building CXX object CMakeFiles/strip-it.dir/src/main.cpp.o
[ 86%] Building CXX object CMakeFiles/strip-it.dir/src/options.cpp.o
[ 90%] Building CXX object CMakeFiles/strip-it.dir/src/counter.cpp.o
[ 95%] Building CXX object CMakeFiles/strip-it.dir/src/calculator.cpp.o
[100%] Linking CXX executable strip-it
CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer.cpp.o: In function `Schuffenhauer::RemoveSidechains(OpenBabel::OBMol*)':
schuffenhauer.cpp:(.text+0xa7): undefined reference to `OpenBabel::OBMol::BeginAtom(__gnu_cxx::__normal_iterator<OpenBabel::OBAtom**, std::vector<OpenBabel::OBAtom*, std::allocator<OpenBabel::OBAtom*> > >&)'
schuffenhauer.cpp:(.text+0xbf): undefined reference to `OpenBabel::OBMol::NextAtom(__gnu_cxx::__normal_iterator<OpenBabel::OBAtom**, std::vector<OpenBabel::OBAtom*, std::allocator<OpenBabel::OBAtom*> > >&)'
CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer.cpp.o: In function `Schuffenhauer::CalculateAcyclicBonds(OpenBabel::OBMol&)':
schuffenhauer.cpp:(.text+0x15f): undefined reference to `OpenBabel::OBMol::BeginBond(__gnu_cxx::__normal_iterator<OpenBabel::OBBond**, std::vector<OpenBabel::OBBond*, std::allocator<OpenBabel::OBBond*> > >&)'
schuffenhauer.cpp:(.text+0x1b9): undefined reference to `OpenBabel::OBMol::NextBond(__gnu_cxx::__normal_iterator<OpenBabel::OBBond**, std::vector<OpenBabel::OBBond*, std::allocator<OpenBabel::OBBond*> > >&)'
CMakeFiles/strip-it.dir/src/scaffolds/schuffenhauer.cpp.o: In function `Schuffenhauer::CalculateHeteroAtoms(OpenBabel::OBMol&, OpenBabel::OBRing*, int)':
schuffenhauer.cpp:(.text+0x224): undefined reference to `OpenBabel::OBMol::BeginAtom(__gnu_cxx::__normal_iterator<OpenBabel::OBAtom**, std::vector<OpenBabel::OBAtom*, std::allocator<OpenBabel::OBAtom*> > >&)'
schuffenhauer.cpp:(.text+0x266): undefined reference to `OpenBabel::OBMol::NextAtom(__gnu_cxx::__normal_iterator<OpenBabel::OBAtom**, std::vector<OpenBabel::OBAtom*, std::allocator<OpenBabel::OBAtom*> > >&)
....
....
....
urcko_1.cpp:(.text+0x320): undefined reference to `OpenBabel::OBMol::BeginBond(__gnu_cxx::__normal_iterator<OpenBabel::OBBond**, std::vector<OpenBabel::OBBond*, std::allocator<OpenBabel::OBBond*> > >&)'
murcko_1.cpp:(.text+0x343): undefined reference to `OpenBabel::OBMol::NextBond(__gnu_cxx::__normal_iterator<OpenBabel::OBBond**, std::vector<OpenBabel::OBBond*, std::allocator<OpenBabel::OBBond*> > >&)'
collect2: error: ld returned 1 exit status
CMakeFiles/strip-it.dir/build.make:615: recipe for target 'strip-it' failed
make[2]: *** [strip-it] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/strip-it.dir/all' failed
make[1]: *** [CMakeFiles/strip-it.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2


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