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mattions / neuronvisio

A Graphical User Interface with 3D Visualization features for NEURON simulation enviroment
https://neuronvisio.readthedocs.io
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conda create -n neuronvisio_env neuronvisio -c mattions - does not work #63

Open orena1 opened 7 years ago

orena1 commented 7 years ago

Hello, I have tried to get neuronvisio working. I tried to use the conda method, conda create -n neuronvisio_env neuronvisio -c mattions but this is what I get:

(neuronvisio_env) oren.amsalem@bream ~ $ neuronvisio
neuronvisio
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-56217a6d174f> in <module>()
----> 1 from neuronvisio.controls import Controls

/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env/lib/python2.7/site-packages/neuronvisio/controls.py in <module>()
     40 
     41 os.environ['ETS_TOOLKIT'] = 'qt4'
---> 42 from pyface.qt import QtGui, QtCore
     43 from PyQt4 import uic
     44 

/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env/lib/python2.7/site-packages/pyface/qt/__init__.py in <module>()
     35             qt_api = 'pyqt'
     36         except ImportError:
---> 37             raise ImportError('Cannot import PySide or PyQt4')
     38 
     39 elif qt_api == 'pyqt':

ImportError: Cannot import PySide or PyQt4
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-5e268e4c48ce> in <module>()
----> 1 controls = Controls()

NameError: name 'Controls' is not defined

Thanks, Oren.

mattions commented 7 years ago

Hi Oren,

it looks like you are missing both PySide and PyQt4 packages.

Without them it is not possbile to create the Controls class, because it depends on them.

HIH, Michele

On 29 May 2017 at 07:31, Oren Amsalem notifications@github.com wrote:

Hello, I have tried to get neuronvisio working. I tried to use the conda method but this is what I get:

(neuronvisio_env) oren.amsalem@bream ~ $ neuronvisio neuronvisio NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015 See http://www.neuron.yale.edu/neuron/credits

ImportError Traceback (most recent call last)

in () ----> 1 from neuronvisio.controls import Controls /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env/lib/python2.7/site-packages/neuronvisio/controls.py in () 40 41 os.environ['ETS_TOOLKIT'] = 'qt4' ---> 42 from pyface.qt import QtGui, QtCore 43 from PyQt4 import uic 44 /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env/lib/python2.7/site-packages/pyface/qt/__init__.py in () 35 qt_api = 'pyqt' 36 except ImportError: ---> 37 raise ImportError('Cannot import PySide or PyQt4') 38 39 elif qt_api == 'pyqt': ImportError: Cannot import PySide or PyQt4 --------------------------------------------------------------------------- NameError Traceback (most recent call last) in () ----> 1 controls = Controls() NameError: name 'Controls' is not defined Thanks, Oren. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread .
orena1 commented 7 years ago

I understand, but I used your conda envierment conda create -n neuronvisio_env neuronvisio -c mattions doesn't it suppose to install all the requirements?

Thanks Michele.

mattions commented 7 years ago

hi @orena1 , yes, it should get all your dependencies.

try from an ipython to do

 from pyface.qt import QtGui, QtCore

if that works, your installation of QT should be good.

I've tried to install Neuronvisio on my laptop using the same command (this runs Python 2, so you need conda for python 2.)

After the install I had to set up the NEURONHOME variable like this:

export NEURONHOME=~/.pyenv/versions/miniconda2-latest/envs/neuronvisio_env/share/nrn/

Note that your env will vary.

After I activate the enviroment, I seem to miss NEURON itself. The PyQt4 bit work for me ok.

Consider that I used Neuronvisio last time back in 2012, and then I did not really use it anymore, so I'm not sure everything should work as expected.

orena1 commented 7 years ago

Thanks, I tried importing pyqt

ipython
Python 2.7.13 | packaged by conda-forge | (default, May  2 2017, 12:48:11) 
Type "copyright", "credits" or "license" for more information.

IPython 5.3.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: from pyface.qt import QtGui, QtCore
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-07f741aae0c2> in <module>()
----> 1 from pyface.qt import QtGui, QtCore

/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env/lib/python2.7/site-packages/pyface/qt/__init__.py in <module>()
     35             qt_api = 'pyqt'
     36         except ImportError:
---> 37             raise ImportError('Cannot import PySide or PyQt4')
     38 
     39 elif qt_api == 'pyqt':

ImportError: Cannot import PySide or PyQt4

I wonder why the conda did not install pyqt correctly.

mattions commented 7 years ago

What is the output of the installation?

orena1 commented 7 years ago 
Fetching package metadata ...........
Solving package specifications: ..........

Package plan for installation in environment /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    gstreamer-1.8.0            |                2         3.4 MB  conda-forge
    ipython-5.4.1              |           py27_0         1.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         4.4 MB

The following NEW packages will be INSTALLED:

    apptools:                           4.4.0-py27_0      conda-forge
    backports.shutil_get_terminal_size: 1.0.0-py27_1      conda-forge
    backports_abc:                      0.5-py27_0        conda-forge
    bzip2:                              1.0.6-1           conda-forge
    ca-certificates:                    2017.4.17-0       conda-forge
    certifi:                            2017.4.17-py27_0  conda-forge
    configobj:                          5.0.6-py27_0                 
    cycler:                             0.10.0-py27_0     conda-forge
    dbus:                               1.10.10-3         conda-forge
    decorator:                          4.0.11-py27_0     conda-forge
    enum34:                             1.1.6-py27_1      conda-forge
    envisage:                           4.5.1-py27_0      conda-forge
    expat:                              2.1.0-2           conda-forge
    fontconfig:                         2.12.1-4          conda-forge
    freetype:                           2.7-1             conda-forge
    functools32:                        3.2.3.2-py27_1    conda-forge
    future:                             0.16.0-py27_0     conda-forge
    gettext:                            0.19.7-1          conda-forge
    glib:                               2.51.4-0          conda-forge
    gst-plugins-base:                   1.8.0-0           conda-forge
    gstreamer:                          1.8.0-2           conda-forge
    hdf5:                               1.8.17-11         conda-forge
    icu:                                58.1-1            conda-forge
    ipython:                            5.4.1-py27_0      conda-forge
    ipython_genutils:                   0.2.0-py27_0      conda-forge
    iv:                                 19-0              mattions   
    jpeg:                               9b-0              conda-forge
    jsoncpp:                            0.10.6-1          conda-forge
    libffi:                             3.2.1-3           conda-forge
    libgfortran:                        3.0.0-1                      
    libiconv:                           1.14-4            conda-forge
    libpng:                             1.6.28-0          conda-forge
    libtiff:                            4.0.6-7           conda-forge
    libxcb:                             1.12-1            conda-forge
    libxml2:                            2.9.4-4           conda-forge
    lzo:                                2.06-0                       
    matplotlib:                         2.0.2-np112py27_0 conda-forge
    mayavi:                             4.5.0-np112py27_1 conda-forge
    mkl:                                2017.0.1-0                   
    ncurses:                            5.9-10            conda-forge
    neuron:                             7.4-py27_0        mattions   
    neuronvisio:                        0.9.1-py27_0      mattions   
    numexpr:                            2.6.2-np112py27_0 conda-forge
    numpy:                              1.12.1-py27_0                
    openssl:                            1.0.2k-0          conda-forge
    pathlib2:                           2.2.1-py27_0      conda-forge
    pcre:                               8.39-0            conda-forge
    pexpect:                            4.2.1-py27_0      conda-forge
    pickleshare:                        0.7.3-py27_0      conda-forge
    pip:                                9.0.1-py27_0      conda-forge
    prompt_toolkit:                     1.0.14-py27_0     conda-forge
    ptyprocess:                         0.5.1-py27_0      conda-forge
    pyface:                             5.1.0-py27_0      conda-forge
    pygments:                           2.2.0-py27_0      conda-forge
    pyparsing:                          2.2.0-py27_0      conda-forge
    pyqt:                               5.6.0-py27_3      conda-forge
    pytables:                           3.4.2-np112py27_0 conda-forge
    python:                             2.7.13-1          conda-forge
    python-dateutil:                    2.6.0-py27_0      conda-forge
    pytz:                               2017.2-py27_0     conda-forge
    qt:                                 5.6.2-2           conda-forge
    readline:                           6.2-0             conda-forge
    scandir:                            1.5-py27_1        conda-forge
    setuptools:                         33.1.1-py27_0     conda-forge
    simplegeneric:                      0.8.1-py27_0      conda-forge
    singledispatch:                     3.4.0.3-py27_0    conda-forge
    sip:                                4.18-py27_1       conda-forge
    six:                                1.10.0-py27_1     conda-forge
    sqlite:                             3.13.0-1          conda-forge
    ssl_match_hostname:                 3.5.0.1-py27_1    conda-forge
    subprocess32:                       3.2.7-py27_0      conda-forge
    tk:                                 8.5.19-1          conda-forge
    tornado:                            4.5.1-py27_0      conda-forge
    traitlets:                          4.3.2-py27_0      conda-forge
    traits:                             4.6.0-py27_1      conda-forge
    traitsui:                           5.1.0-py27_0      conda-forge
    vtk:                                7.1.0-py27_3      conda-forge
    wcwidth:                            0.1.7-py27_0      conda-forge
    wheel:                              0.29.0-py27_0     conda-forge
    xorg-libxau:                        1.0.8-3           conda-forge
    xorg-libxdmcp:                      1.1.2-3           conda-forge
    xz:                                 5.2.2-0           conda-forge
    zlib:                               1.2.11-0          conda-forge

Proceed ([y]/n)? y

Fetching packages ...
gstreamer-1.8. 100% |##############################################################################################################################| Time: 0:00:23 149.75 kB/s
ipython-5.4.1- 100% |##############################################################################################################################| Time: 0:00:08 126.31 kB/s
Extracting packages ...
[      COMPLETE      ]|#################################################################################################################################################| 100%
Linking packages ...
[fontconfig          ]|##################################################################                                                                               '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/cprop.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/cprop.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ivocmain.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/ivocmain.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libIVhines.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libIVhines.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so.3' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libIVhines.so.3'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so.3.0.3' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libIVhines.so.3.0.3'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libivoc.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libivoc.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libivoc.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libivoc.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmemacs.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmemacs.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmemacs.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmemacs.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmeschach.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmeschach.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmeschach.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libmeschach.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libneuron_gnu.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libneuron_gnu.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libneuron_gnu.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libneuron_gnu.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrniv.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrniv.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrniv.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrniv.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnmpi.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnmpi.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnmpi.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnmpi.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnoc.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnoc.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnoc.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnoc.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnpython.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnpython.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnpython.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libnrnpython.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/liboc.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/liboc.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/liboc.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/liboc.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libocxt.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libocxt.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libocxt.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libocxt.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libreadline.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libreadline.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libreadline.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libreadline.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libscopmath.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libscopmath.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libscopmath.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libscopmath.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsparse13.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsparse13.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsparse13.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsparse13.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsundials.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsundials.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsundials.so.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so.0.0.0' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libsundials.so.0.0.0'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.la' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libUnidrawhines.la'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libUnidrawhines.so'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so.3' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libUnidrawhines.so.3'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so.3.0.3' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/libUnidrawhines.so.3.0.3'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnconf.h' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/nrnconf.h'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnmain.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/nrnmain.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnnoiv.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/nrnnoiv.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nvkludge.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/nvkludge.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ocmain.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/ocmain.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ocnoiv.o' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib/ocnoiv.o'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/bbswork.sh' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/bbswork.sh'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/hel2mos1.sh' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/hel2mos1.sh'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/iclass' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/iclass'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/idemo' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/idemo'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/idraw' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/idraw'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/ivoc' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/ivoc'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/memacs' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/memacs'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mkthreadsafe' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/mkthreadsafe'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/modlunit' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/modlunit'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mos2nrn' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/mos2nrn'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mos2nrn2.sh' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/mos2nrn2.sh'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/neurondemo' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/neurondemo'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nocmodl' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nocmodl'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrngui' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrngui'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrniv' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrniv'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrniv_makefile' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrniv_makefile'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnivmodl' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnivmodl'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnmech_makefile' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnmech_makefile'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnoc' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnoc'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnoc_makefile' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnoc_makefile'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnocmodl' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnocmodl'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnpyenv.sh' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/nrnpyenv.sh'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/oc' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/oc'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/set_nrnpyenv.sh' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/set_nrnpyenv.sh'
'/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/sortspike' -> '/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin/sortspike'
[      COMPLETE      ]|#################################################################################################################################################| 100%
Linking files from /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/lib to /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/cprop.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ivocmain.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so.3
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libIVhines.so.3.0.3
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libivoc.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmemacs.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libmeschach.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libneuron_gnu.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrniv.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnmpi.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnoc.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libnrnpython.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/liboc.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libocxt.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so
/home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so does exist. Removing for linking
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libreadline.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libscopmath.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsparse13.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libsundials.so.0.0.0
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.la
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so.3
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/libUnidrawhines.so.3.0.3
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnconf.h
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnmain.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nrnnoiv.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/nvkludge.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ocmain.o
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/lib/ocnoiv.o
Linking files from /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/x86_64/bin to /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/bbswork.sh
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/hel2mos1.sh
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/iclass
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/idemo
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/idraw
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/ivoc
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/memacs
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mkthreadsafe
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/modlunit
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mos2nrn
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/mos2nrn2.sh
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/neurondemo
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nocmodl
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrngui
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrniv
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrniv_makefile
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnivmodl
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnmech_makefile
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnoc
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnoc_makefile
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnocmodl
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/nrnpyenv.sh
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/oc
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/set_nrnpyenv.sh
Analyzing file /home/ls/users/oren.amsalem/anaconda2/envs/neuronvisio_env1/bin/sortspike
#
# To activate this environment, use:
# > source activate neuronvisio_env1
#
# To deactivate this environment, use:
# > source deactivate neuronvisio_env1
#

Thanks

mattions commented 7 years ago

Did you activate the enviroment running the source command?