#9 Error on make

[Vito S.]

When I try to make pharmit using the instructions provided, it fails with the following:

[ 95%] Building CXX object CMakeFiles/pharmit.dir/shapedb/packers/SpectralPacker.cpp.o
[ 97%] Building CXX object CMakeFiles/pharmit.dir/CommandLine2/CommandLine.cpp.o
[100%] Linking CXX executable pharmit
/home/spadavec/itx/smina-code/build/libsmina.a(grid.cpp.o): In function `_GLOBAL__sub_I__ZNK4grid8evaluateERK4atomRK3vecddPS3_':
grid.cpp:(.text.startup+0xdd): undefined reference to `boost::system::generic_category()'
grid.cpp:(.text.startup+0xe2): undefined reference to `boost::system::generic_category()'
grid.cpp:(.text.startup+0xe7): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(PDBQTUtilities.cpp.o): In function `boost::system::error_category::std_category::equivalent(std::error_code const&, int) const':
PDBQTUtilities.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0x40): undefined reference to `boost::system::generic_category()'
PDBQTUtilities.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xb9): undefined reference to `boost::system::generic_category()'
PDBQTUtilities.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0x111): undefined reference to `boost::system::generic_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(PDBQTUtilities.cpp.o): In function `boost::system::error_category::std_category::equivalent(int, std::error_condition const&) const':
PDBQTUtilities.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0x3f): undefined reference to `boost::system::generic_category()'
PDBQTUtilities.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0xd1): undefined reference to `boost::system::generic_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(PDBQTUtilities.cpp.o):PDBQTUtilities.cpp:(.text.startup+0xdd): more undefined references to `boost::system::generic_category()' follow
/home/spadavec/itx/smina-code/build/libsmina.a(PDBQTUtilities.cpp.o): In function `_GLOBAL__sub_I__Z13FindFragmentsN9OpenBabel5OBMolERSt6vectorIS1_IiSaIiEESaIS3_EE':
PDBQTUtilities.cpp:(.text.startup+0xe7): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(SminaConverter.cpp.o): In function `_GLOBAL__sub_I__ZN14SminaConverter14MCMolConverterC2ERN9OpenBabel5OBMolE':
SminaConverter.cpp:(.text.startup+0x2d): undefined reference to `boost::system::generic_category()'
SminaConverter.cpp:(.text.startup+0x32): undefined reference to `boost::system::generic_category()'
SminaConverter.cpp:(.text.startup+0x37): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(model.cpp.o): In function `_GLOBAL__sub_I__ZN15smina_atom_type4dataE':
model.cpp:(.text.startup+0x7): undefined reference to `boost::system::generic_category()'
model.cpp:(.text.startup+0xc): undefined reference to `boost::system::generic_category()'
model.cpp:(.text.startup+0x11): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(parse_pdbqt.cpp.o): In function `_GLOBAL__sub_I__Z27set_fixed_rotable_hydrogensb':
parse_pdbqt.cpp:(.text.startup+0x7): undefined reference to `boost::system::generic_category()'
parse_pdbqt.cpp:(.text.startup+0xc): undefined reference to `boost::system::generic_category()'
parse_pdbqt.cpp:(.text.startup+0x11): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(quaternion.cpp.o): In function `_GLOBAL__sub_I__Z2eqRKN5boost4math10quaternionIdEES4_':
quaternion.cpp:(.text.startup+0x2b): undefined reference to `boost::system::generic_category()'
quaternion.cpp:(.text.startup+0x30): undefined reference to `boost::system::generic_category()'
quaternion.cpp:(.text.startup+0x35): undefined reference to `boost::system::system_category()'
/home/spadavec/itx/smina-code/build/libsmina.a(random.cpp.o): In function `_GLOBAL__sub_I__Z9random_flddRN5boost6random23mersenne_twister_engineIjLm32ELm624ELm397ELm31ELj2567483615ELm11ELj4294967295ELm7ELj2636928640ELm15ELj4022730752ELm18ELj1812433253EEE':
random.cpp:(.text.startup+0x2b): undefined reference to `boost::system::generic_category()'
random.cpp:(.text.startup+0x30): undefined reference to `boost::system::generic_category()'
random.cpp:(.text.startup+0x35): undefined reference to `boost::system::system_category()'
collect2: error: ld returned 1 exit status
CMakeFiles/pharmit.dir/build.make:818: recipe for target 'pharmit' failed
make[2]: *** [pharmit] Error 1
CMakeFiles/Makefile2:82: recipe for target 'CMakeFiles/pharmit.dir/all' failed
make[1]: *** [CMakeFiles/pharmit.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2

Not sure what I'm doing wrong?

[David Koes]

Looks like you are missing the boost system library or are linking against a different version than you compiled headers with.