Dear all,
I've been facing some issues when trying to compile OB 3.1.1 on my linux
cluster (rocks clusters, gcc 4.8.2).
Cmake goes well with:
$ cmake -DCMAKE_INSTALL_PREFIX=/home/cjoliveira/tools/openbabel3
-DEIGEN3_INCLUDE_DIR=/share/apps/eigen3 /share/apps/openbabel-3.1.1/
Compilation starts fine, as copied below. I get a warning about
std::binder1st, but the problems show up during the linking. The message
seems to be similar to some functions not being included in the Makefile to
generate the shared library libopenbabel.so.
For the sake of comparison, I tested compiling OB 3.0.0 using the same
flags and everything went fine. Any ideas about what may be going on?
Thanks in advance,
Alessandro
...
[ 4%] Built target coordgen
[ 4%] Linking CXX shared library ../../../lib/libmaeparser.so
[ 4%] Built target maeparser
...
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o
[ 17%] Linking C shared library ../../../lib/libinchi.so
[ 17%] Built target inchi
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o
...
[ 23%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o
[ 24%] Building CXX object
src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o
/share/apps/iMcLiBELa/src/openbabel-3.1.1/src/stereo/perception.cpp: In
function 'void OpenBabel::ImplicitRefToStereo(OpenBabel::OBMol&,
OpenBabel::OBStereo::Ref, OpenBabel::OBStereo::Ref)':
/share/apps/iMcLiBELa/src/openbabel-3.1.1/src/stereo/perception.cpp:3005:57:
warning: 'binder1st' is deprecated (declared at
/share/apps/gcc/4.8.2/include/c++/4.8.2/backward/binders.h:104)
[-Wdeprecated-declarations]
const std::binder1st<std::equal_to<OBStereo::Ref> >
equal_to_implicitRef = std::bind1st (equal_to<OBStereo::Ref>(),
(OBStereo::Ref) OBStereo::ImplicitRef);
^
[ 24%] Linking CXX shared library ../lib/libopenbabel.so
CMakeFiles/openbabel.dir/mol.cpp.o: In function
`OpenBabel::OBMol::CorrectForPH(double)':
mol.cpp:(.text+0x1e8c): undefined reference to `_ZTHN9OpenBabel7phmodelE'
CMakeFiles/openbabel.dir/mol.cpp.o: In function
`OpenBabel::OBMol::PerceiveBondOrders()':
mol.cpp:(.text+0x11956): undefined reference to `_ZTHN9OpenBabel9bondtyperE'
CMakeFiles/openbabel.dir/atom.cpp.o: In function
`OpenBabel::OBAtom::GetType()':
atom.cpp:(.text+0x5f1): undefined reference to `_ZTHN9OpenBabel9atomtyperE'
CMakeFiles/openbabel.dir/atom.cpp.o: In function
`OpenBabel::OBAtom::GetHyb() const':
atom.cpp:(.text+0x6b9): undefined reference to `_ZTHN9OpenBabel9atomtyperE'
CMakeFiles/openbabel.dir/atom.cpp.o: In function
`OpenBabel::OBAtom::GetPartialCharge()':
atom.cpp:(.text+0x75d): undefined reference to `_ZTHN9OpenBabel7phmodelE'
collect2: error: ld returned 1 exit status
--
*****************************************************************
* Alessandro S. Nascimento *
* Associate Professor - Sao Carlos Institute of Physics *
* University of São Paulo (IFSC/USP) *
* Phone: +55-16-3364-8075 *
* E-mail: asnascime...@ifsc.usp.br *
*****************************************************************
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