Dear Nick,
I have installed sisl manually by "$> python setup.py install" as you said.
But the mentioned error appeared again in the terminal. I attach the
installation log file.
Best Regards,
On Sun, May 28, 2017 at 12:41 AM, Nick Papior <nickpap...@gmail.com> wrote:
> It seems like you are installing using pip?
>
> As I mentioned in the previous mail, you should download the tarball and
> install sisl manually by using this command:
>
> $> python setup.py install
>
> If this is indeed what you did, could you please attach the entire
> installation log.
>
> 2017-05-27 7:54 GMT+02:00 maryam jamaati <m.sjama...@gmail.com>:
>
>> Dear Nick,
>>
>> Thank you for your help.
>> I have installed sisl package. It was installed completely and correctly
>> as you can see in the below:
>>
>>
>> " Installed /usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linu
>> x-i686.egg
>> Processing dependencies for sisl==0.8.3
>> Searching for netCDF4==1.2.7
>> Best match: netCDF4 1.2.7
>> Adding netCDF4 1.2.7 to easy-install.pth file
>> Installing ncinfo script to /usr/local/bin
>> Installing nc4tonc3 script to /usr/local/bin
>> Installing nc3tonc4 script to /usr/local/bin
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for scipy==0.19.0
>> Best match: scipy 0.19.0
>> Adding scipy 0.19.0 to easy-install.pth file
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for numpy==1.12.1
>> Best match: numpy 1.12.1
>> Adding numpy 1.12.1 to easy-install.pth file
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for setuptools==3.3
>> Best match: setuptools 3.3
>> Adding setuptools 3.3 to easy-install.pth file
>> Installing easy_install script to /usr/local/bin
>> Installing easy_install-2.7 script to /usr/local/bin
>>
>> Using /usr/lib/python2.7/dist-packages
>> Searching for six==1.10.0
>> Best match: six 1.10.0
>> Adding six 1.10.0 to easy-install.pth file
>>
>> Using /home/sf/.local/lib/python2.7/site-packages
>> Finished processing dependencies for sisl==0.8.3"
>>
>> *But unfortunately*, when I run the code the *below error *appears:
>>
>> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
>> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
>> when used with get_resource_filename. Consider a more secure location (set
>> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
>> warnings.warn(msg, UserWarning)
>> Traceback (most recent call last):
>> File "convert-tshs-nc.py", line 5, in <module>
>> H = sisl.get_sile(sys.argv[1]).read_es()
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89,
>> in read_es
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50,
>> in read_geom
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35,
>> in read_sc
>> ValueError: failed to create intent(cache|hide)|optional array— must have
>> defined dimensions but got (3,0,)
>>
>> Best Regards,
>>
>> Maryam Jamaati
>>
>>
>> On Wed, May 24, 2017 at 11:21 AM, Nick Papior <nickpap...@gmail.com>
>> wrote:
>>
>>> I haven't tried the fortran extensions through pip.
>>>
>>> Could you please try and install sisl the manual way?
>>> Download the tar-ball and issue:
>>>
>>> python setup.py install
>>>
>>>
>>> 2017-05-23 10:09 GMT+02:00 maryam jamaati <m.sjama...@gmail.com>:
>>>
>>>> Dear Nick,
>>>>
>>>> thanks for your attention.
>>>> I installed sisl via pip command. And it was successfully installed
>>>> without any errors.
>>>> Also i installed pre-requisite before installing sisl such as :
>>>> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>>>>
>>>> Best Regards,
>>>>
>>>> On Mon, May 22, 2017 at 5:44 PM, Nick Papior <nickpap...@gmail.com>
>>>> wrote:
>>>>
>>>>> Could you tell us how you have installed sisl?
>>>>>
>>>>> Also, I think I made a mistake in the script, it should be:
>>>>>
>>>>> >>> script begin <<<
>>>>> #!/usr/bin/env python
>>>>> import sys
>>>>> import sisl
>>>>> # Read the electronic structure from the file
>>>>> H = sisl.get_sile(sys.argv[1]).read_es()
>>>>> H.write('output.nc')
>>>>> >>> script end <<<
>>>>>
>>>>> 2017-05-21 7:26 GMT+02:00 maryam jamaati <m.sjama...@gmail.com>:
>>>>>
>>>>>> Dear siesta users,
>>>>>>
>>>>>> In order to convert from TSHS to nc we used this small script from (
>>>>>> https://answers.launchpad.net/siesta/+question/435947):
>>>>>>
>>>>>> #!/usr/bin/env python
>>>>>> import sys
>>>>>> import sisl
>>>>>> # Read the electronic structure from the file
>>>>>> H = get_sile(sys.argv[1]).read_es()
>>>>>> H.write('output.nc')
>>>>>> »> script end «<
>>>>>>
>>>>>> and then call it by:
>>>>>> python convert.py siesta.TSHS
>>>>>>
>>>>>>
>>>>>>
>>>>>> But after running the code, the below error appears:
>>>>>> ValueError: failed to create intent(cache|hide)|optional array— must
>>>>>> have defined dimensions but got (3,0,)
>>>>>>
>>>>>> I would be pleased if anyone could help me to solve this problem.
>>>>>>
>>>>>> Best Regards,
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Kind regards Nick
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>
>
> --
> Kind regards Nick
>
sf@sf-Lenovo-IdeaPad-Z510:~/sisl-0.8.3$ sudo python setup.py install
system_info:
NOT AVAILABLE
running install
running bdist_egg
running egg_info
running build_src
build_src
building py_modules sources
building extension "sisl.io.siesta._siesta" sources
f2py options: []
adding 'build/src.linux-i686-2.7/fortranobject.c' to sources.
adding 'build/src.linux-i686-2.7' to include_dirs.
building data_files sources
build_src: building npy-pkg config files
writing requirements to sisl.egg-info/requires.txt
writing sisl.egg-info/PKG-INFO
writing top-level names to sisl.egg-info/top_level.txt
writing dependency_links to sisl.egg-info/dependency_links.txt
writing entry points to sisl.egg-info/entry_points.txt
reading manifest file 'sisl.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'sisl.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-i686/egg
running install_lib
running build_py
copying sisl/info.py -> build/lib.linux-i686-2.7/sisl
copying build/src.linux-i686-2.7/sisl/__config__.py ->
build/lib.linux-i686-2.7/sisl
copying build/src.linux-i686-2.7/sisl/io/__config__.py ->
build/lib.linux-i686-2.7/sisl/io
copying build/src.linux-i686-2.7/sisl/io/wannier/__config__.py ->
build/lib.linux-i686-2.7/sisl/io/wannier
copying build/src.linux-i686-2.7/sisl/io/gulp/__config__.py ->
build/lib.linux-i686-2.7/sisl/io/gulp
copying build/src.linux-i686-2.7/sisl/io/vasp/__config__.py ->
build/lib.linux-i686-2.7/sisl/io/vasp
copying build/src.linux-i686-2.7/sisl/io/siesta/__config__.py ->
build/lib.linux-i686-2.7/sisl/io/siesta
copying build/src.linux-i686-2.7/sisl/io/bigdft/__config__.py ->
build/lib.linux-i686-2.7/sisl/io/bigdft
copying build/src.linux-i686-2.7/sisl/quantity/__config__.py ->
build/lib.linux-i686-2.7/sisl/quantity
copying build/src.linux-i686-2.7/sisl/utils/__config__.py ->
build/lib.linux-i686-2.7/sisl/utils
copying build/src.linux-i686-2.7/sisl/shape/__config__.py ->
build/lib.linux-i686-2.7/sisl/shape
copying build/src.linux-i686-2.7/sisl/geom/__config__.py ->
build/lib.linux-i686-2.7/sisl/geom
copying build/src.linux-i686-2.7/sisl/units/__config__.py ->
build/lib.linux-i686-2.7/sisl/units
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
creating build/bdist.linux-i686/egg
creating build/bdist.linux-i686/egg/sisl
creating build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/xyz.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/__config__.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/xsf.py ->
build/bdist.linux-i686/egg/sisl/io
creating build/bdist.linux-i686/egg/sisl/io/wannier
copying build/lib.linux-i686-2.7/sisl/io/wannier/__config__.py ->
build/bdist.linux-i686/egg/sisl/io/wannier
copying build/lib.linux-i686-2.7/sisl/io/wannier/seedname.py ->
build/bdist.linux-i686/egg/sisl/io/wannier
copying build/lib.linux-i686-2.7/sisl/io/wannier/setup.py ->
build/bdist.linux-i686/egg/sisl/io/wannier
copying build/lib.linux-i686-2.7/sisl/io/wannier/sile.py ->
build/bdist.linux-i686/egg/sisl/io/wannier
copying build/lib.linux-i686-2.7/sisl/io/wannier/__init__.py ->
build/bdist.linux-i686/egg/sisl/io/wannier
creating build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/__config__.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/hessian.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/got.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/setup.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/sile.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/gulp/__init__.py ->
build/bdist.linux-i686/egg/sisl/io/gulp
copying build/lib.linux-i686-2.7/sisl/io/cube.py ->
build/bdist.linux-i686/egg/sisl/io
creating build/bdist.linux-i686/egg/sisl/io/vasp
copying build/lib.linux-i686-2.7/sisl/io/vasp/__config__.py ->
build/bdist.linux-i686/egg/sisl/io/vasp
copying build/lib.linux-i686-2.7/sisl/io/vasp/setup.py ->
build/bdist.linux-i686/egg/sisl/io/vasp
copying build/lib.linux-i686-2.7/sisl/io/vasp/sile.py ->
build/bdist.linux-i686/egg/sisl/io/vasp
copying build/lib.linux-i686-2.7/sisl/io/vasp/__init__.py ->
build/bdist.linux-i686/egg/sisl/io/vasp
copying build/lib.linux-i686-2.7/sisl/io/vasp/car.py ->
build/bdist.linux-i686/egg/sisl/io/vasp
creating build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/bands.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/xv.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/out.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/_siesta.so ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/__config__.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/fdf.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/tbtrans.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/tbtrans_av.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/tbtrans_proj.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/binaries.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/siesta.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/siesta_grid.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/setup.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/sile.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/siesta/__init__.py ->
build/bdist.linux-i686/egg/sisl/io/siesta
copying build/lib.linux-i686-2.7/sisl/io/setup.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/sile.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/table.py ->
build/bdist.linux-i686/egg/sisl/io
creating build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/bigdft/__config__.py ->
build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/bigdft/setup.py ->
build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/bigdft/sile.py ->
build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/bigdft/ascii.py ->
build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/bigdft/__init__.py ->
build/bdist.linux-i686/egg/sisl/io/bigdft
copying build/lib.linux-i686-2.7/sisl/io/ham.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/molden.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/_help.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/io/__init__.py ->
build/bdist.linux-i686/egg/sisl/io
copying build/lib.linux-i686-2.7/sisl/sparse.py ->
build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/info.py -> build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/grid.py -> build/bdist.linux-i686/egg/sisl
creating build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/__config__.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/dynmat.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/hamiltonian.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/self_energy.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/setup.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/quantity/__init__.py ->
build/bdist.linux-i686/egg/sisl/quantity
copying build/lib.linux-i686-2.7/sisl/__config__.py ->
build/bdist.linux-i686/egg/sisl
creating build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/ranges.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/__config__.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/misc.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/sdata.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/cmd.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/setup.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/__init__.py ->
build/bdist.linux-i686/egg/sisl/utils
copying build/lib.linux-i686-2.7/sisl/utils/c2f.py ->
build/bdist.linux-i686/egg/sisl/utils
creating build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/ellipsoid.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/__config__.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/shape.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/setup.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/prism4.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/shape/__init__.py ->
build/bdist.linux-i686/egg/sisl/shape
copying build/lib.linux-i686-2.7/sisl/quaternion.py ->
build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/atom.py -> build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/supercell.py ->
build/bdist.linux-i686/egg/sisl
creating build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/__config__.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/nanotube.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/special.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/setup.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/flat.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/basic.py ->
build/bdist.linux-i686/egg/sisl/geom
copying build/lib.linux-i686-2.7/sisl/geom/__init__.py ->
build/bdist.linux-i686/egg/sisl/geom
creating build/bdist.linux-i686/egg/sisl/units
copying build/lib.linux-i686-2.7/sisl/units/__config__.py ->
build/bdist.linux-i686/egg/sisl/units
copying build/lib.linux-i686-2.7/sisl/units/siesta.py ->
build/bdist.linux-i686/egg/sisl/units
copying build/lib.linux-i686-2.7/sisl/units/setup.py ->
build/bdist.linux-i686/egg/sisl/units
copying build/lib.linux-i686-2.7/sisl/units/__init__.py ->
build/bdist.linux-i686/egg/sisl/units
copying build/lib.linux-i686-2.7/sisl/setup.py ->
build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/geometry.py ->
build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/_help.py ->
build/bdist.linux-i686/egg/sisl
copying build/lib.linux-i686-2.7/sisl/__init__.py ->
build/bdist.linux-i686/egg/sisl
byte-compiling build/bdist.linux-i686/egg/sisl/io/xyz.py to xyz.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/xsf.py to xsf.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/wannier/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/wannier/seedname.py to
seedname.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/wannier/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/wannier/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/wannier/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/hessian.py to hessian.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/got.py to got.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/gulp/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/cube.py to cube.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/vasp/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/vasp/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/vasp/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/vasp/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/vasp/car.py to car.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/bands.py to bands.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/xv.py to xv.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/out.py to out.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/fdf.py to fdf.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/tbtrans.py to
tbtrans.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/tbtrans_av.py to
tbtrans_av.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/tbtrans_proj.py to
tbtrans_proj.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py to
binaries.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/siesta.py to siesta.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/siesta_grid.py to
siesta_grid.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/table.py to table.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/bigdft/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/bigdft/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/bigdft/sile.py to sile.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/bigdft/ascii.py to ascii.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/bigdft/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/ham.py to ham.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/molden.py to molden.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/_help.py to _help.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/io/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/sparse.py to sparse.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/info.py to info.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/grid.py to grid.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/dynmat.py to dynmat.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/hamiltonian.py to
hamiltonian.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/self_energy.py to
self_energy.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quantity/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/__config__.py to __config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/ranges.py to ranges.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/misc.py to misc.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/sdata.py to sdata.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/cmd.py to cmd.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/utils/c2f.py to c2f.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/ellipsoid.py to
ellipsoid.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/shape.py to shape.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/prism4.py to prism4.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/shape/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/quaternion.py to quaternion.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/atom.py to atom.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/supercell.py to supercell.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/nanotube.py to nanotube.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/special.py to special.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/flat.py to flat.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/basic.py to basic.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geom/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/units/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/units/siesta.py to siesta.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/units/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/units/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/setup.py to setup.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/geometry.py to geometry.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/_help.py to _help.pyc
byte-compiling build/bdist.linux-i686/egg/sisl/__init__.py to __init__.pyc
creating stub loader for sisl/io/siesta/_siesta.so
byte-compiling build/bdist.linux-i686/egg/sisl/io/siesta/_siesta.py to
_siesta.pyc
installing package data to build/bdist.linux-i686/egg
running install_data
creating build/bdist.linux-i686/egg/sisl/geom/tests
copying sisl/geom/tests/test_geom.py ->
build/bdist.linux-i686/egg/sisl/geom/tests/
creating build/bdist.linux-i686/egg/sisl/shape/tests
copying sisl/shape/tests/test_prism4.py ->
build/bdist.linux-i686/egg/sisl/shape/tests/
copying sisl/shape/tests/test_ellipsoid.py ->
build/bdist.linux-i686/egg/sisl/shape/tests/
creating build/bdist.linux-i686/egg/sisl/tests
copying sisl/tests/test_quaternion.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_atom.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_sgeom.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_package.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_geometry.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_sparse.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_supercell.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_grid.py -> build/bdist.linux-i686/egg/sisl/tests/
copying sisl/tests/test_geometry_return.py ->
build/bdist.linux-i686/egg/sisl/tests/
creating build/bdist.linux-i686/egg/sisl/units/tests
copying sisl/units/tests/test_siesta.py ->
build/bdist.linux-i686/egg/sisl/units/tests/
copying sisl/units/tests/test_units.py ->
build/bdist.linux-i686/egg/sisl/units/tests/
creating build/bdist.linux-i686/egg/sisl/quantity/tests
copying sisl/quantity/tests/test_self_energy.py ->
build/bdist.linux-i686/egg/sisl/quantity/tests/
copying sisl/quantity/tests/test_dynmat.py ->
build/bdist.linux-i686/egg/sisl/quantity/tests/
copying sisl/quantity/tests/test_hamiltonian.py ->
build/bdist.linux-i686/egg/sisl/quantity/tests/
creating build/bdist.linux-i686/egg/sisl/io/tests
copying sisl/io/tests/test_siesta.py ->
build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/common.py -> build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/test_fdf.py -> build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/test_object.py ->
build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/test_tb.py -> build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/test_xyz.py -> build/bdist.linux-i686/egg/sisl/io/tests/
copying sisl/io/tests/test_xv.py -> build/bdist.linux-i686/egg/sisl/io/tests/
creating build/bdist.linux-i686/egg/sisl/utils/tests
copying sisl/utils/tests/test_misc.py ->
build/bdist.linux-i686/egg/sisl/utils/tests/
copying sisl/utils/tests/test_c2f.py ->
build/bdist.linux-i686/egg/sisl/utils/tests/
copying sisl/utils/tests/test_ranges.py ->
build/bdist.linux-i686/egg/sisl/utils/tests/
running install_clib
customize UnixCCompiler
creating build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/PKG-INFO -> build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/SOURCES.txt -> build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/dependency_links.txt ->
build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/entry_points.txt -> build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/requires.txt -> build/bdist.linux-i686/egg/EGG-INFO
copying sisl.egg-info/top_level.txt -> build/bdist.linux-i686/egg/EGG-INFO
writing build/bdist.linux-i686/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating 'dist/sisl-0.8.3-py2.7-linux-i686.egg' and adding
'build/bdist.linux-i686/egg' to it
removing 'build/bdist.linux-i686/egg' (and everything under it)
Processing sisl-0.8.3-py2.7-linux-i686.egg
Copying sisl-0.8.3-py2.7-linux-i686.egg to
/usr/local/lib/python2.7/dist-packages
Adding sisl 0.8.3 to easy-install.pth file
Installing sgrid script to /usr/local/bin
Installing sgeom script to /usr/local/bin
Installing sdata script to /usr/local/bin
Installed /usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linux-i686.egg
Processing dependencies for sisl==0.8.3
Searching for netCDF4==1.2.7
Best match: netCDF4 1.2.7
Adding netCDF4 1.2.7 to easy-install.pth file
Installing ncinfo script to /usr/local/bin
Installing nc4tonc3 script to /usr/local/bin
Installing nc3tonc4 script to /usr/local/bin
Using /usr/local/lib/python2.7/dist-packages
Searching for scipy==0.19.0
Best match: scipy 0.19.0
Adding scipy 0.19.0 to easy-install.pth file
Using /usr/local/lib/python2.7/dist-packages
Searching for numpy==1.12.1
Best match: numpy 1.12.1
Adding numpy 1.12.1 to easy-install.pth file
Using /usr/local/lib/python2.7/dist-packages
Searching for setuptools==3.3
Best match: setuptools 3.3
Adding setuptools 3.3 to easy-install.pth file
Installing easy_install script to /usr/local/bin
Installing easy_install-2.7 script to /usr/local/bin
Using /usr/lib/python2.7/dist-packages
Searching for six==1.10.0
Best match: six 1.10.0
Adding six 1.10.0 to easy-install.pth file
Using /home/sf/.local/lib/python2.7/site-packages
Finished processing dependencies for sisl==0.8.3
sf@sf-Lenovo-IdeaPad-Z510:~/sisl-0.8.3$
