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theochem / horton

HORTON: Helpful Open-source Research TOol for N-fermion systems
http://theochem.github.io/horton/
GNU General Public License v3.0
94 stars 40 forks source link

No module named cext #293

Open SomeAnonimCoder opened 3 years ago

SomeAnonimCoder commented 3 years ago

Code from this repo, master branch. How I installed it:

(py2) [root@Ventum horton]# python setup.py install
PLATFORM=Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-centos-7.6.1810-Core
LIBXC Configuration
   File setup.cfg not found. Skipping.
   From environment variables
      -
   Static lib config in ${QAWORKDIR}
      extra_objects: ['/home/xray/libxc/lib/libxc.a']
      include_dirs: ['/home/xray/libxc/include']
   Final
      extra_objects: ['/home/xray/libxc/lib/libxc.a']
      include_dirs: ['/home/xray/libxc/include']
LIBINT2 Configuration
   File setup.cfg not found. Skipping.
   From environment variables
      -
   Static lib not found in ${QAWORKDIR}
      extra_objects: ['qaworkdir/cached/libint-2.0.3/lib/libint2.a']
      include_dirs: ['qaworkdir/cached/libint-2.0.3/include/libint2']
   pkg-config failed.
   Last resort fallback plan
      include_dirs: ['/usr/include/libint2']
      libraries: ['int2']
   Final
      include_dirs: ['/usr/include/libint2']
      libraries: ['int2']
Version of dependencies:
             breathe: -- not found --
            coverage: Coverage.py, version 3.6b3.  http://nedbatchelder.com/code/coverage/3.6b3
            cppcheck: -- not found --
                curl: curl 7.29.0 (x86_64-redhat-linux-gnu) libcurl/7.29.0 NSS/3.36 zlib/1.2.7 libidn/1.28 libssh2/1.4.3
              cython: Cython version 0.29.14
            docutils: -- not found --
             doxygen: -- not found --
                 gcc: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
                 git: git version 1.8.3.1
           gitpython: -- not found --
                h5py: -- not found --
          matplotlib: -- not found --
                nose: nosetests version 1.3.7
               numpy: 1.16.6
                 pip: pip 19.3.1 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/pip (python 2.7)
         pycodestyle: -- not found --
          pydocstyle: -- not found --
              pylint: 
              python: Python 2.7.18 :: Anaconda, Inc.
               scipy: -- not found --
              sphinx: -- not found --
    sphinx_rtd_theme: -- not found --
               sympy: -- not found --
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/horton
copying horton/constants.py -> build/lib.linux-x86_64-2.7/horton
copying horton/moments.py -> build/lib.linux-x86_64-2.7/horton
copying horton/periodic.py -> build/lib.linux-x86_64-2.7/horton
copying horton/units.py -> build/lib.linux-x86_64-2.7/horton
copying horton/quadprog.py -> build/lib.linux-x86_64-2.7/horton
copying horton/exceptions.py -> build/lib.linux-x86_64-2.7/horton
copying horton/utils.py -> build/lib.linux-x86_64-2.7/horton
copying horton/log.py -> build/lib.linux-x86_64-2.7/horton
copying horton/context.py -> build/lib.linux-x86_64-2.7/horton
copying horton/__init__.py -> build/lib.linux-x86_64-2.7/horton
copying horton/cache.py -> build/lib.linux-x86_64-2.7/horton
creating build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_examples.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_quadprog.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_cache.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_periodic.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_moments.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_log.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_cell.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_utils.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/test_context.py -> build/lib.linux-x86_64-2.7/horton/test
copying horton/test/common.py -> build/lib.linux-x86_64-2.7/horton/test
creating build/lib.linux-x86_64-2.7/horton/espfit
copying horton/espfit/cost.py -> build/lib.linux-x86_64-2.7/horton/espfit
copying horton/espfit/__init__.py -> build/lib.linux-x86_64-2.7/horton/espfit
creating build/lib.linux-x86_64-2.7/horton/espfit/test
copying horton/espfit/test/test_mask.py -> build/lib.linux-x86_64-2.7/horton/espfit/test
copying horton/espfit/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/espfit/test
copying horton/espfit/test/test_cext.py -> build/lib.linux-x86_64-2.7/horton/espfit/test
copying horton/espfit/test/test_cost.py -> build/lib.linux-x86_64-2.7/horton/espfit/test
creating build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/iobas.py -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/gobasis.py -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/__init__.py -> build/lib.linux-x86_64-2.7/horton/gbasis
creating build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_gbw.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_iobas.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_common.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_gobasis.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_iter.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_boys.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_ints.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_cholesky.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_fns.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
copying horton/gbasis/test/test_cartpure.py -> build/lib.linux-x86_64-2.7/horton/gbasis/test
creating build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/ode2.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/molgrid.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/base.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/visual.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/utils.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/radial.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/__init__.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/poisson.py -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/atgrid.py -> build/lib.linux-x86_64-2.7/horton/grid
creating build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_visual.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_becke.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_rtransform.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_base.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_ode2.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_atgrid.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_lebedev_laikov.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_poisson.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_utils.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_radial.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_cubic_spline.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_uniform.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/test_molgrid.py -> build/lib.linux-x86_64-2.7/horton/grid/test
copying horton/grid/test/common.py -> build/lib.linux-x86_64-2.7/horton/grid/test
creating build/lib.linux-x86_64-2.7/horton/io
copying horton/io/lockedh5.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/xyz.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/iodata.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/molpro.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/utils.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/molden.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/cube.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/wfn.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/__init__.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/gaussian.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/internal.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/vasp.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/cp2k.py -> build/lib.linux-x86_64-2.7/horton/io
copying horton/io/molekel.py -> build/lib.linux-x86_64-2.7/horton/io
creating build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_wfn.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_molpro.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_molden.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_cp2k.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_internal.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_vasp.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_lockedh5.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_gaussian.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_cube.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_molekel.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_iodata.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/test_xyz.py -> build/lib.linux-x86_64-2.7/horton/io/test
copying horton/io/test/common.py -> build/lib.linux-x86_64-2.7/horton/io/test
creating build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/rotate.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/bond_order.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf_oda.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/occ.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/response.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/observable.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/indextransform.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/project.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf_ediis2.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf_ediis.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/builtin.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/convergence.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/hamiltonian.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/gridgroup.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/utils.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/libxc.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf_diis.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/__init__.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/guess.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/orbitals.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf.py -> build/lib.linux-x86_64-2.7/horton/meanfield
copying horton/meanfield/scf_cdiis.py -> build/lib.linux-x86_64-2.7/horton/meanfield
creating build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_orbitals.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_scf.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_libxc.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_guess.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_occ.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_bond_order.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_scf_cdiis.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_gridgroup.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_project.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_hamiltonian.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_indextransform.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_scf_ediis.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_observable.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_scf_ediis2.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_builtin.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_scf_oda.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_rotate.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_utils.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/test_response.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
copying horton/meanfield/test/common.py -> build/lib.linux-x86_64-2.7/horton/meanfield/test
creating build/lib.linux-x86_64-2.7/horton/part
copying horton/part/iterstock.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/base.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/hirshfeld.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/mulliken.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/proatomdb.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/__init__.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/hirshfeld_i.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/stockholder.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/becke.py -> build/lib.linux-x86_64-2.7/horton/part
copying horton/part/mbis.py -> build/lib.linux-x86_64-2.7/horton/part
creating build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_becke.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_mbis.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_wpart.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_mulliken.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_base.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/test_proatomdb.py -> build/lib.linux-x86_64-2.7/horton/part/test
copying horton/part/test/common.py -> build/lib.linux-x86_64-2.7/horton/part/test
creating build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/atomdb.py -> build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/hdf2csv.py -> build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/__init__.py -> build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/wpart.py -> build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/espfit.py -> build/lib.linux-x86_64-2.7/horton/scripts
copying horton/scripts/common.py -> build/lib.linux-x86_64-2.7/horton/scripts
creating build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_common.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_atomdb.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_wpart.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_convert.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/__init___.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_espfit.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_hdf2csv.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/test_cubehead.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
copying horton/scripts/test/common.py -> build/lib.linux-x86_64-2.7/horton/scripts/test
creating build/lib.linux-x86_64-2.7/horton/modelhamiltonians
copying horton/modelhamiltonians/__init__.py -> build/lib.linux-x86_64-2.7/horton/modelhamiltonians
copying horton/modelhamiltonians/physmodham.py -> build/lib.linux-x86_64-2.7/horton/modelhamiltonians
creating build/lib.linux-x86_64-2.7/horton/modelhamiltonians/test
copying horton/modelhamiltonians/test/test_hubbard.py -> build/lib.linux-x86_64-2.7/horton/modelhamiltonians/test
copying horton/modelhamiltonians/test/__init__.py -> build/lib.linux-x86_64-2.7/horton/modelhamiltonians/test
copying horton/moments.pxd -> build/lib.linux-x86_64-2.7/horton
copying horton/nucpot.pxd -> build/lib.linux-x86_64-2.7/horton
copying horton/cext.pxd -> build/lib.linux-x86_64-2.7/horton
copying horton/cell.pxd -> build/lib.linux-x86_64-2.7/horton
copying horton/espfit/mask.pxd -> build/lib.linux-x86_64-2.7/horton/espfit
copying horton/espfit/electrostatics.pxd -> build/lib.linux-x86_64-2.7/horton/espfit
copying horton/gbasis/gbw.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/iter_gb.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/gbasis.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/common.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/fns.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/cholesky.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/iter_pow.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/ints.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/boys.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/gbasis/cartpure.pxd -> build/lib.linux-x86_64-2.7/horton/gbasis
copying horton/grid/lebedev_laikov.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/utils.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/evaluate.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/ode2.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/rtransform.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/becke.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/cext.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/cubic_spline.pxd -> build/lib.linux-x86_64-2.7/horton/grid
copying horton/grid/uniform.pxd -> build/lib.linux-x86_64-2.7/horton/grid
running build_ext
skipping 'horton/cext.cpp' Cython extension (up-to-date)
skipping 'horton/gbasis/cext.cpp' Cython extension (up-to-date)
skipping 'horton/grid/cext.cpp' Cython extension (up-to-date)
skipping 'horton/meanfield/cext.cpp' Cython extension (up-to-date)
skipping 'horton/espfit/cext.cpp' Cython extension (up-to-date)
building 'horton.cext' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/horton
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/nucpot.cpp -o build/temp.linux-x86_64-2.7/horton/nucpot.o -std=c++11
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/moments.cpp -o build/temp.linux-x86_64-2.7/horton/moments.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/cell.cpp -o build/temp.linux-x86_64-2.7/horton/cell.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/cext.cpp -o build/temp.linux-x86_64-2.7/horton/cext.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from horton/cext.cpp:617:
/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
g++ -pthread -shared -B /home/xray/anaconda3/envs/py2/compiler_compat -L/home/xray/anaconda3/envs/py2/lib -Wl,-rpath=/home/xray/anaconda3/envs/py2/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/horton/nucpot.o build/temp.linux-x86_64-2.7/horton/moments.o build/temp.linux-x86_64-2.7/horton/cell.o build/temp.linux-x86_64-2.7/horton/cext.o -L/home/xray/anaconda3/envs/py2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/horton/cext.so
building 'horton.gbasis.cext' extension
creating build/temp.linux-x86_64-2.7/horton/gbasis
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/cartpure.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/cartpure.o -std=c++11
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/iter_pow.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/iter_pow.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/ints.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/ints.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/calc.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/calc.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/boys.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/boys.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
horton/gbasis/ints.cpp: In member function ‘virtual void GB4IntegralLibInt::add(double, double, double, double, double, const double*, const double*, const double*, const double*)’:
horton/gbasis/ints.cpp:687:16: warning: unused variable ‘qd’ [-Wunused-variable]
   const double qd[3] = {
                ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/gbw.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/gbw.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
horton/gbasis/boys.cpp: In function ‘void boys_function_array(long int, double, double*)’:
horton/gbasis/boys.cpp:114:37: warning: ‘xs[5]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+6][i]*xs[5];
                                     ^
horton/gbasis/boys.cpp:113:37: warning: ‘xs[4]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+5][i]*xs[4] +
                                     ^
horton/gbasis/boys.cpp:112:37: warning: ‘xs[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+4][i]*xs[3] +
                                     ^
horton/gbasis/boys.cpp:111:37: warning: ‘xs[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+3][i]*xs[2] +
                                     ^
horton/gbasis/boys.cpp:110:37: warning: ‘xs[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+2][i]*xs[1] +
                                     ^
horton/gbasis/boys.cpp:109:37: warning: ‘xs[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 boys_fn_data[m+1][i]*xs[0] +
                                     ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/gbasis.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/gbasis.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from ./horton/gbasis/gbasis.h:27:0,
                 from ./horton/gbasis/gbw.h:26,
                 from horton/gbasis/gbw.cpp:22:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/iter_gb.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/iter_gb.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from ./horton/gbasis/gbasis.h:27:0,
                 from horton/gbasis/gbasis.cpp:31:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
In file included from ./horton/gbasis/gbasis.h:27:0,
                 from ./horton/gbasis/iter_gb.h:26,
                 from horton/gbasis/iter_gb.cpp:25:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/common.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/common.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/fns.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/fns.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from horton/gbasis/fns.cpp:33:0:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/cholesky.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/cholesky.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from ./horton/gbasis/gbasis.h:27:0,
                 from ./horton/gbasis/gbw.h:26,
                 from ./horton/gbasis/cholesky.h:27,
                 from horton/gbasis/cholesky.cpp:25:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/gbasis/cext.cpp -o build/temp.linux-x86_64-2.7/horton/gbasis/cext.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from horton/gbasis/cext.cpp:612:
/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/libint2 -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/moments.cpp -o build/temp.linux-x86_64-2.7/horton/moments.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from horton/gbasis/cext.cpp:622:0:
./horton/gbasis/fns.h: In constructor ‘GB1ExpGridOrbGradientFn::GB1ExpGridOrbGradientFn(long int, long int, long int*, long int)’:
./horton/gbasis/fns.h:349:8: warning: ‘GB1ExpGridOrbGradientFn::offset_h1’ will be initialized after [-Wreorder]
   long offset_h1;  //!< Higher offset for the polynomials for the gradient.
        ^
./horton/gbasis/fns.h:344:9: warning:   ‘long int* GB1ExpGridOrbGradientFn::iorbs’ [-Wreorder]
   long* iorbs;     //!< Array of indices of orbitals to be evaluated on grid.
         ^
./horton/gbasis/fns.h:326:12: warning:   when initialized here [-Wreorder]
   explicit GB1ExpGridOrbGradientFn(long max_shell_type, long nfn, long* iorbs, long norb)
            ^
g++ -pthread -shared -B /home/xray/anaconda3/envs/py2/compiler_compat -L/home/xray/anaconda3/envs/py2/lib -Wl,-rpath=/home/xray/anaconda3/envs/py2/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/horton/gbasis/cartpure.o build/temp.linux-x86_64-2.7/horton/gbasis/iter_pow.o build/temp.linux-x86_64-2.7/horton/gbasis/ints.o build/temp.linux-x86_64-2.7/horton/gbasis/calc.o build/temp.linux-x86_64-2.7/horton/gbasis/boys.o build/temp.linux-x86_64-2.7/horton/gbasis/gbw.o build/temp.linux-x86_64-2.7/horton/gbasis/gbasis.o build/temp.linux-x86_64-2.7/horton/gbasis/iter_gb.o build/temp.linux-x86_64-2.7/horton/gbasis/common.o build/temp.linux-x86_64-2.7/horton/gbasis/fns.o build/temp.linux-x86_64-2.7/horton/gbasis/cholesky.o build/temp.linux-x86_64-2.7/horton/gbasis/cext.o build/temp.linux-x86_64-2.7/horton/moments.o -L/home/xray/anaconda3/envs/py2/lib -lint2 -lpython2.7 -o build/lib.linux-x86_64-2.7/horton/gbasis/cext.so
building 'horton.grid.cext' extension
creating build/temp.linux-x86_64-2.7/horton/grid
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/lebedev_laikov.cpp -o build/temp.linux-x86_64-2.7/horton/grid/lebedev_laikov.o -std=c++11
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/ode2.cpp -o build/temp.linux-x86_64-2.7/horton/grid/ode2.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/cubic_spline.cpp -o build/temp.linux-x86_64-2.7/horton/grid/cubic_spline.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
horton/grid/cubic_spline.cpp: In function ‘void tridiagsym_solve(double*, double*, double*, double*, int)’:
horton/grid/cubic_spline.cpp:66:59: warning: ‘tmp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         double denominator = (diag_mid[i] - diag_up[i - 1]*tmp1);
                                                           ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/rtransform.cpp -o build/temp.linux-x86_64-2.7/horton/grid/rtransform.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/evaluate.cpp -o build/temp.linux-x86_64-2.7/horton/grid/evaluate.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/utils.cpp -o build/temp.linux-x86_64-2.7/horton/grid/utils.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/becke.cpp -o build/temp.linux-x86_64-2.7/horton/grid/becke.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/uniform.cpp -o build/temp.linux-x86_64-2.7/horton/grid/uniform.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/cext.cpp -o build/temp.linux-x86_64-2.7/horton/grid/cext.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from horton/grid/cext.cpp:612:
/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/cell.cpp -o build/temp.linux-x86_64-2.7/horton/cell.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/moments.cpp -o build/temp.linux-x86_64-2.7/horton/moments.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
g++ -pthread -shared -B /home/xray/anaconda3/envs/py2/compiler_compat -L/home/xray/anaconda3/envs/py2/lib -Wl,-rpath=/home/xray/anaconda3/envs/py2/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/horton/grid/lebedev_laikov.o build/temp.linux-x86_64-2.7/horton/grid/ode2.o build/temp.linux-x86_64-2.7/horton/grid/cubic_spline.o build/temp.linux-x86_64-2.7/horton/grid/rtransform.o build/temp.linux-x86_64-2.7/horton/grid/evaluate.o build/temp.linux-x86_64-2.7/horton/grid/utils.o build/temp.linux-x86_64-2.7/horton/grid/becke.o build/temp.linux-x86_64-2.7/horton/grid/uniform.o build/temp.linux-x86_64-2.7/horton/grid/cext.o build/temp.linux-x86_64-2.7/horton/cell.o build/temp.linux-x86_64-2.7/horton/moments.o -L/home/xray/anaconda3/envs/py2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/horton/grid/cext.so
building 'horton.meanfield.cext' extension
creating build/temp.linux-x86_64-2.7/horton/meanfield
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/libxc/include -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/meanfield/cext.cpp -o build/temp.linux-x86_64-2.7/horton/meanfield/cext.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from horton/meanfield/cext.cpp:612:
/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
g++ -pthread -shared -B /home/xray/anaconda3/envs/py2/compiler_compat -L/home/xray/anaconda3/envs/py2/lib -Wl,-rpath=/home/xray/anaconda3/envs/py2/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/horton/meanfield/cext.o /home/xray/libxc/lib/libxc.a -L/home/xray/anaconda3/envs/py2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/horton/meanfield/cext.so
building 'horton.espfit.cext' extension
creating build/temp.linux-x86_64-2.7/horton/espfit
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/espfit/mask.cpp -o build/temp.linux-x86_64-2.7/horton/espfit/mask.o -std=c++11
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/espfit/electrostatics.cpp -o build/temp.linux-x86_64-2.7/horton/espfit/electrostatics.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/espfit/cext.cpp -o build/temp.linux-x86_64-2.7/horton/espfit/cext.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from horton/espfit/cext.cpp:612:
/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/cell.cpp -o build/temp.linux-x86_64-2.7/horton/cell.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /home/xray/anaconda3/envs/py2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/numpy/core/include -I. -I/home/xray/anaconda3/envs/py2/include/python2.7 -c horton/grid/uniform.cpp -o build/temp.linux-x86_64-2.7/horton/grid/uniform.o -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
g++ -pthread -shared -B /home/xray/anaconda3/envs/py2/compiler_compat -L/home/xray/anaconda3/envs/py2/lib -Wl,-rpath=/home/xray/anaconda3/envs/py2/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/horton/espfit/mask.o build/temp.linux-x86_64-2.7/horton/espfit/electrostatics.o build/temp.linux-x86_64-2.7/horton/espfit/cext.o build/temp.linux-x86_64-2.7/horton/cell.o build/temp.linux-x86_64-2.7/horton/grid/uniform.o -L/home/xray/anaconda3/envs/py2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/horton/espfit/cext.so
running build_scripts
creating build/scripts-2.7
copying and adjusting scripts/horton-esp-test.py -> build/scripts-2.7
copying and adjusting scripts/horton-cubehead.py -> build/scripts-2.7
copying and adjusting scripts/horton-esp-cost.py -> build/scripts-2.7
copying and adjusting scripts/horton-atomdb.py -> build/scripts-2.7
copying and adjusting scripts/horton-esp-fit.py -> build/scripts-2.7
copying and adjusting scripts/horton-wpart.py -> build/scripts-2.7
copying and adjusting scripts/horton-hdf2csv.py -> build/scripts-2.7
copying and adjusting scripts/horton-regression-test.py -> build/scripts-2.7
copying and adjusting scripts/horton-convert.py -> build/scripts-2.7
copying and adjusting scripts/horton-esp-gen.py -> build/scripts-2.7
changing mode of build/scripts-2.7/horton-esp-test.py from 644 to 755
changing mode of build/scripts-2.7/horton-cubehead.py from 644 to 755
changing mode of build/scripts-2.7/horton-esp-cost.py from 644 to 755
changing mode of build/scripts-2.7/horton-atomdb.py from 644 to 755
changing mode of build/scripts-2.7/horton-esp-fit.py from 644 to 755
changing mode of build/scripts-2.7/horton-wpart.py from 644 to 755
changing mode of build/scripts-2.7/horton-hdf2csv.py from 644 to 755
changing mode of build/scripts-2.7/horton-regression-test.py from 644 to 755
changing mode of build/scripts-2.7/horton-convert.py from 644 to 755
changing mode of build/scripts-2.7/horton-esp-gen.py from 644 to 755
running install_lib
copying build/lib.linux-x86_64-2.7/horton/gbasis/cext.so -> /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton/gbasis
copying build/lib.linux-x86_64-2.7/horton/espfit/cext.so -> /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton/espfit
copying build/lib.linux-x86_64-2.7/horton/cext.so -> /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton
copying build/lib.linux-x86_64-2.7/horton/meanfield/cext.so -> /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton/meanfield
copying build/lib.linux-x86_64-2.7/horton/grid/cext.so -> /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton/grid
running install_headers
running install_scripts
copying build/scripts-2.7/horton-esp-test.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-cubehead.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-esp-cost.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-atomdb.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-esp-fit.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-wpart.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-hdf2csv.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-regression-test.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-convert.py -> /home/xray/anaconda3/envs/py2/bin
copying build/scripts-2.7/horton-esp-gen.py -> /home/xray/anaconda3/envs/py2/bin
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-esp-test.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-cubehead.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-esp-cost.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-atomdb.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-esp-fit.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-wpart.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-hdf2csv.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-regression-test.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-convert.py to 755
changing mode of /home/xray/anaconda3/envs/py2/bin/horton-esp-gen.py to 755
running install_data
install_dir=/home/xray/anaconda3/envs/py2
Creating /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton/data_dir.txt
running install_egg_info
Removing /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton-2.1.0-py2.7.egg-info
Writing /home/xray/anaconda3/envs/py2/lib/python2.7/site-packages/horton-2.1.0-py2.7.egg-info

Seems to be no errors, but...

(py2) [root@Ventum horton]# python
Python 2.7.18 |Anaconda, Inc.| (default, Apr 23 2020, 22:42:48) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from horton import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "horton/__init__.py", line 28, in <module>
    from horton.cext import *
ImportError: No module named cext

What is this and how can I fix it?

tovrstra commented 3 years ago

Could you try running your python interpreter in a different directory than the source tree? That may fix it.