Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
I followed the instructions from the INSTALL file in the extracted avogadro-1.1.1 folder.
cmake ../ worked correctly for me, except that it did not found doxygen:
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
Then, true problems arise with make -j2.
It has to be noticed that even if the version is claimed to be compatible with eigen3
-- Eigen 2.0.x or later (3.x also supported)
it is not the case because of path problems. With eigen3, the installation stopped at 0% because it did not found <eigen/core>. I had to remove eigen3 and use eigen2 to advance to some point.
But even with that, it stopped at 10%, as shown here:
[ 0%] [ 0%] Generating moc_elementcolor.cxx
Generating ui_bsdysettingswidget.h
[ 0%] Generating moc_bsdyengine.cxx
Scanning dependencies of target elementcolor
[ 0%] Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o
Scanning dependencies of target bsdyengine
[ 0%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o
[ 0%] Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/moc_elementcolor.cxx.o
Linking CXX static library elementcolor.a
[ 0%] Built target elementcolor
[ 0%] Generating qrc_navigatetool.cxx
[ 0%] Generating moc_navigatetool.cxx
[ 0%] Generating ui_navigatesettingswidget.h
Scanning dependencies of target navigatetool
[ 0%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o
[ 0%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o
[ 0%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o
Linking CXX static library bsdyengine.a
[ 0%] Built target bsdyengine
Scanning dependencies of target spglib
[ 0%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/cell.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/debug.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/hall_symbol.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/lattice.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/mathfunc.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/pointgroup.c.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/primitive.c.o
[ 1%] [ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/refinement.c.o
Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/moc_navigatetool.cxx.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spacegroup.c.o
[ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spg_database.c.o
[ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o
[ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry.c.o
[ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry_kpoint.c.o
[ 3%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/qrc_navigatetool.cxx.o
Linking CXX static library navigatetool.a
[ 3%] Built target navigatetool
[ 3%] Generating moc_slaterset.cxx
[ 3%] Generating moc_basisset.cxx
[ 3%] Generating moc_gaussianset.cxx
Scanning dependencies of target OpenQube
Linking C static library libspglib.a
[ 3%] Built target spglib
Scanning dependencies of target tubegen
[ 3%] [ 3%] Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Bitmap.c.o
Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o
[ 3%] Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Core3DMath.c.o
[ 3%] Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/eprintf.c.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/ANSR.cpp.o
[ 3%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basisset.cpp.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Cell.cpp.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/CrystalCell.cpp.o
[ 3%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basissetloader.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/diamond.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/fcc.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/graphite.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubeGen.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/cube.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubuleBasis.cpp.o
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o
Linking CXX static library libtubegen.a
[ 5%] Built target tubegen
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessus.cpp.o
[ 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
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molden.cpp.o
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/mopacaux.cpp.o
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/slaterset.cpp.o
[ 6%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/moc_basisset.cxx.o
[ 6%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/moc_gaussianset.cxx.o
[ 6%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/moc_slaterset.cxx.o
[ 6%] Generating libavogadro_ja.qm
Linking CXX shared library ../../../../../lib/libavogadro_OpenQube.so
[ 6%] Built target OpenQube
[ 6%] Generating moc_animation.cxx
[ 6%] Generating moc_atom.cxx
[ 6%] Generating moc_bond.cxx
[ 6%] Generating moc_color.cxx
[ 6%] Generating moc_colorbutton.cxx
[ 6%] Generating moc_cube.cxx
[ 6%] Generating moc_dockextension.cxx
[ 7%] Generating moc_dockwidget.cxx
[ 7%] Generating moc_elementdetail_p.cxx
[ 7%] Generating moc_elementtranslator.cxx
[ 7%] Generating moc_engine.cxx
[ 7%] Generating moc_extension.cxx
[ 7%] Generating moc_fragment.cxx
[ 7%] Generating moc_glwidget.cxx
[ 8%] Generating moc_mesh.cxx
[ 8%] Generating moc_meshgenerator.cxx
[ 8%] Generating moc_molecule.cxx
[ 8%] Generating moc_moleculefile.cxx
[ 8%] Generating moc_periodictablescene_p.cxx
[ 8%] Generating moc_periodictableview.cxx
[ 8%] Generating moc_plotwidget.cxx
[ 8%] Generating moc_plugin.cxx
[ 9%] Generating moc_pluginmanager.cxx
[ 9%] Generating moc_primitive.cxx
[ 9%] Generating moc_protein.cxx
[ 9%] Generating moc_readfilethread_p.cxx
[ 9%] Generating moc_residue.cxx
[ 9%] Generating moc_textmatrixeditor.cxx
[ 9%] Generating moc_tool.cxx
[ 9%] Generating moc_toolgroup.cxx
[ 10%] Generating moc_zmatrix.cxx
[ 10%] Generating libavogadro_sl.qm
```~~
Actually no error happened, it just lasted forever at the last line without reacting.
Now I don't know how to fix it and I suspect an internal compatibility problem with openbabel or Qt4 or something, and with ubuntu 13.10.
Thanks in advance.
Reported by: *anonymous
I tried to install avogadro-1.1.1 from tar.bz2 file (link: http://sourceforge.net/projects/avogadro/?source=typ_redirect) on my Ubuntu 13.10 64-bit owner system.
I followed the instructions from the INSTALL file in the extracted avogadro-1.1.1 folder.
cmake ../ worked correctly for me, except that it did not found doxygen:
Then, true problems arise with make -j2.
It has to be noticed that even if the version is claimed to be compatible with eigen3
it is not the case because of path problems. With eigen3, the installation stopped at 0% because it did not found <eigen/core>. I had to remove eigen3 and use eigen2 to advance to some point.
But even with that, it stopped at 10%, as shown here: