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Dear all,
while compiling on amd64 laptop with ubuntu 7.10 i get an error regarindg openbabel during the linking step. This happens with the pre-installed openbabel-2.0 as well as with the 2.1.1 I compiled myself.
Should I build 2.0 or 2.1 with special options?
The error is this:
Linking CXX executable dist/bin/Molekel
CMakeFiles/Molekel.dir/utility/System.o: In function `GetTemporaryFileName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
System.cpp:(.text+0x43e): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat15WriteChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::WriteChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat14ReadChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
collect2: ld returned 1 exit status
make[2]: *** [dist/bin/Molekel] Error 1
make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2
make: *** [all] Error 2
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Dear all,
while compiling on amd64 laptop with ubuntu 7.10 i get an error regarindg openbabel during the linking step. This happens with the pre-installed openbabel-2.0 as well as with the 2.1.1 I compiled myself.
Should I build 2.0 or 2.1 with special options?
The error is this:
Linking CXX executable dist/bin/Molekel
CMakeFiles/Molekel.dir/utility/System.o: In function `GetTemporaryFileName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
System.cpp:(.text+0x43e): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat15WriteChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::WriteChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat14ReadChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
collect2: ld returned 1 exit status
make[2]: *** [dist/bin/Molekel] Error 1
make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2
make: *** [all] Error 2
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Hi,
how are you building OpenBabel (static or dynamic) ? you need to build it as a dynamic library.
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I'm now at work, and cannot check but it should be dynamic. The configure of opebabel ny dedafult shuld build dynamic and static libs (--enable-shared[=PKGS] build shared libraries [default=yes]). I cannot think of anyone reason to have build static libs but maybe I need to specify --enable-shared. Anyway I have tried the repository version of Ubuntu (ver 2.0.2, and it should be dynamic) with the same error.
Anyway I'll try to rebuild openbabel with explicit --enable-shared and tell you the outcome.
Thanks
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hi,
i tried to reinstall using openbabel-2.0.2 (Ihave read on this forum to use 2.0.x rather than 2.1.x) with --enable-shared but without success; the error is:
CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridLabels() const':
MolekelMolecule.cpp:(.text+0x2859): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::HasGridData() const':
MolekelMolecule.cpp:(.text+0x7a04): undefined reference to `OpenBabel::OBMol::HasData(char const*)'
MolekelMolecule.cpp:(.text+0x7a1d): undefined reference to `OpenBabel::OBMol::HasData(char const*)'
CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataStepSize(double*) const':
MolekelMolecule.cpp:(.text+0x7acc): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
MolekelMolecule.cpp:(.text+0x7b6f): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataNumSteps(int*) const':
MolekelMolecule.cpp:(.text+0x7c72): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
MolekelMolecule.cpp:(.text+0x7ccf): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataMin(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
MolekelMolecule.cpp:(.text+0x7d86): undefined reference to `OpenBabel::OBMol::GetData(char const*)'
CMakeFiles/Molekel.dir/MolekelMolecule.o:MolekelMolecule.cpp:(.text+0x7dec): more undefined references to `OpenBabel::OBMol::GetData(char const*)' follow
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OBGridData::OBGridData()':
OBGaussianCubeFormat.cpp:(.text._ZN10OBGridDataC1Ev[OBGridData::OBGridData()]+0x12): undefined reference to `OpenBabel::OBGenericData::OBGenericData()'
CMakeFiles/Molekel.dir/utility/OBT41Format.o: In function `OBT41Data::OBT41Data()':
OBT41Format.cpp:(.text._ZN9OBT41DataC1Ev[OBT41Data::OBT41Data()]+0x12): undefined reference to `OpenBabel::OBGenericData::OBGenericData()'
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