GCC 4.8.2 is known to be problematic with C++ and is also an ancient compiler. https://www.gnu.org/software/gcc/gcc-4.8/
The original release was in 2013 (10 years ago). Please install a more recent version of GCC / G++ Best regards, -Geoff On Jun 8, 2023 at 1:34:12 PM, Alessandro S. Nascimento via OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net> wrote: > 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 * > ***************************************************************** > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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