It seems like there’s a problem with the Eigen libraries. Perhaps eigen2-dev wasn’t installed?
Hope that helps, -Geoff > On Dec 9, 2015, at 5:01 PM, Luciano Costa <[email protected]> wrote: > > Hi dear developers, > > I would like to report here maybe what can be a kind of a bug related to > openbabel > libraries. I already installed avogadro and openbabel from either apt-get or > source and I never had been problems, but since last week I'm trying to fix > the following error. I tried to compile using openbabel-dev source libraries > and also using openbabel from apt-get on Ubuntu 14.04. The configuration was > fine and every library was configured, including openbabel ones. However some > errors are occurring when it is linking with the openbabel libraries. Please, > does anyone has a suggestion about that? What could be that? I tried from > different ways. > > 0%] [ 0%] [ 0%] [ 1%] [ 1%] Generating ui_bsdysettingswidget.h > Generating moc_elementcolor.cxx > Generating qrc_navigatetool.cxx > Generating ui_navigatesettingswidget.h > [ 1%] [ 1%] Generating moc_navigatetool.cxx > [ 1%] Building C object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Bitmap.c.o > Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/cell.c.o > [ 1%] [ 1%] Building C object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Core3DMath.c.o > [ 1%] Generating moc_bsdyengine.cxx > Generating moc_slaterset.cxx > Building C object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/eprintf.c.o > Scanning dependencies of target elementcolor > [ 1%] Building CXX object > libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o > [ 1%] [ 1%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/debug.c.o > Generating moc_basisset.cxx > Scanning dependencies of target navigatetool > [ 1%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/ANSR.cpp.o > Scanning dependencies of target bsdyengine > [ 1%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Cell.cpp.o > [ 1%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/hall_symbol.c.o > [ 1%] [ 1%] Building CXX object > libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o > Generating moc_gaussianset.cxx > [ 1%] Building CXX object > libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp:31:27: > fatal error: openbabel/mol.h: No such file or directory > #include <openbabel/mol.h> > ^ > compilation terminated. > Scanning dependencies of target OpenQube > [ 1%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o > [ 2%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/CrystalCell.cpp.o > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp:39:27: > fatal error: openbabel/mol.h: No such file or directory > #include <openbabel/mol.h> > ^ > compilation terminated. > [ 2%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/lattice.c.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/mathfunc.c.o > [ 3%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/diamond.cpp.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/pointgroup.c.o > make[2]: *** > [libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error > 1 > make[1]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/primitive.c.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/refinement.c.o > [ 3%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/fcc.cpp.o > [ 3%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/graphite.cpp.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spacegroup.c.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spg_database.c.o > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o > make[2]: *** > [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o] Error 1 > make[1]: *** [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/all] Error 2 > [ 3%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry.c.o > [ 4%] Building C object > libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry_kpoint.c.o > [ 4%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubeGen.cpp.o > [ 4%] Building CXX object > libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o > [ 4%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basisset.cpp.o > [ 4%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basissetloader.cpp.o > [ 4%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/cube.cpp.o > [ 4%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o > [ 4%] Building CXX object > libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubuleBasis.cpp.o > Linking C static library libspglib.a > [ 4%] Built target spglib > [ 5%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessus.cpp.o > In file included from > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/navigate.h:30:0, > from > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:31: > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > void setModelview(const Eigen::Transform3d &matrix); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51: > warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive] > void setModelview(const Eigen::Transform3d &matrix); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > const Eigen::Transform3d & modelview() const; > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > Eigen::Transform3d & modelview(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h: > In member function ‘Eigen::Vector3d Avogadro::Camera::V4toV3DivW(const > Vector4d&)’: > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19: > error: ‘const Vector4d’ has no member named ‘start’ > return v4.start<3>()/v4.w(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28: > error: expected primary-expression before ‘)’ token > return v4.start<3>()/v4.w(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp: > In member function ‘void > Avogadro::NavigateTool::computeReferencePoint(Avogadro::GLWidget*)’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:95:57: > error: ‘class Avogadro::Camera’ has no member named ‘modelview’ > Vector3d transformedAtomPos = widget->camera()->modelview() * > *atom->pos(); > ^ > make[2]: *** > [libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o] Error 1 > make[2]: *** Waiting for unfinished jobs.... > [ 5%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianfchk.cpp.o > [ 5%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o > In file included from > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp:29:0: > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > void setModelview(const Eigen::Transform3d &matrix); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51: > warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive] > void setModelview(const Eigen::Transform3d &matrix); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > const Eigen::Transform3d & modelview() const; > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7: > error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type > Eigen::Transform3d & modelview(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h: > In member function ‘Eigen::Vector3d Avogadro::Camera::V4toV3DivW(const > Vector4d&)’: > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19: > error: ‘const Vector4d’ has no member named ‘start’ > return v4.start<3>()/v4.w(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28: > error: expected primary-expression before ‘)’ token > return v4.start<3>()/v4.w(); > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘void OpenQube::GUKBasisSet::outputCoord()’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:90:3: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Coordinates:\n"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘void OpenQube::GUKBasisSet::outputBasis()’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:99:3: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Basis functions" << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:104:5: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Atom(" << i << "): " << shellLabels.at(i) << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:116:7: > error: ‘cout’ is not a member of ‘std’ > std::cout << "shell type " << shells.at(i).at(j) << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:119:9: > error: ‘cout’ is not a member of ‘std’ > std::cout << " e = " << gtoExponents.at(k) << " c = " > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:125:3: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Read in nShell " << nShell << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:126:3: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Read in nBasisFunctions " << nBasisFunctions << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:127:3: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Read in nElectrons " << nElectrons << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘OpenQube::orbital > OpenQube::GUKBasisSet::shellTypeFromString(std::string)’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:179:3: > error: ‘cerr’ is not a member of ‘std’ > std::cerr << "ERROR: shellTypeFromString with label: " << label << > std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘void OpenQube::GamessukOut::GamessukOutNoQt(const > string&, OpenQube::GaussianSet*)’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:205:5: > error: ‘cerr’ is not a member of ‘std’ > std::cerr << "Cannot open: " << filename << "\n"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:225:5: > error: ‘cerr’ is not a member of ‘std’ > std::cerr << "ERROR READING ORBITALS FROM FILE: " << filename << > std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘bool OpenQube::GamessukOut::parseFile(std::ifstream&)’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:266:9: > error: ‘cerr’ is not a member of ‘std’ > std::cerr << "ERROR: can currently only do rhf!\n"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: > In member function ‘void > OpenQube::GamessukOut::readBasisSet(std::ifstream&)’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:480:34: > error: ‘cerr’ is not a member of ‘std’ > if ( tokens.size() != 12 ) std::cerr << "PROBLEM READING SP LINE!\n"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:508:55: > error: ‘cerr’ is not a member of ‘std’ > if (strstr(buffer," total number of shells")==NULL) std::cerr << "Error > reading nShell!: " << line << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:517:54: > error: ‘cerr’ is not a member of ‘std’ > if (strstr(buffer," total number of basis")==NULL) std::cerr << "Error > reading nBasisFunctions!: " << line << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:525:52: > error: ‘cerr’ is not a member of ‘std’ > if (strstr(buffer," number of electrons")==NULL) std::cerr << "Error > reading nElectrons!: " << line << std::endl; > ^ > [ 5%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molden.cpp.o > make[2]: *** > [libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o] Error 1 > make[1]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/all] Error 2 > [ 5%] Building CXX object > libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o > make[2]: *** > [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o] > Error 1 > make[2]: *** Waiting for unfinished jobs.... > Linking CXX static library libtubegen.a > [ 5%] Built target tubegen > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp: > In member function ‘void OpenQube::GaussianSet::outputAll()’: > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:785:7: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Shell " << i << "\tF\n MO 1"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:787:9: > error: ‘cout’ is not a member of ‘std’ > std::cout << "\t" << m_moMatrix(0, m_moIndices[i] + j); > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:788:7: > error: ‘cout’ is not a member of ‘std’ > std::cout << std::endl; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:791:7: > error: ‘cout’ is not a member of ‘std’ > std::cout << "Shell " << i << "\tF7\n MO 1"; > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:793:9: > error: ‘cout’ is not a member of ‘std’ > std::cout << "\t" << m_moMatrix(0, m_moIndices[i] + j); > ^ > /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:794:7: > error: ‘cout’ is not a member of ‘std’ > std::cout << std::endl; > ^ > make[2]: *** > [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o] > Error 1 > make[1]: *** > [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/all] > Error 2 > make: *** [all] Error 2 > > -- > ######################################################### > ** MOLECULAR MODELING AND COMPUTER SIMULATION GROUP ** > http://molmod-cs.weebly.com > > Universidade Federal Fluminense > Campus Valonguinho > Instituto de Química - Departamento de Físico-Química > Outeiro de São João Batista s/n CEP 24020-141 Niterói - RJ > tel: +55 21 2629 2166 (FAX) > +55 21 2629 2232 > +55 21 2629 2171 > > ------------------------------------------------------- > ########################################################## > Luciano Tavares da Costa > e-mail to: [email protected] or [email protected] > > Linux is freedom! > ------------------------------------------------------------------------------ > _______________________________________________ > Avogadro-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/avogadro-devel 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