[FIXED] Spyder doesn't load from Anaconda 3.4

Issue

I've recently just installed Anaconda 3 (for Python 3.4) on a fresh Ubuntu 14.04 installation.

When I go to launch the spyder IDE, I receive following error message:

No module named 'version'
Traceback (most recent call last):
File "/home/daniel/anaconda3/bin/spyder", line 3, in <module>
start_app.main()
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/start_app.py",         line     91, in main
from spyderlib import spyder
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/spyder.py", line 158,  in <module>
from spyderlib.utils.environ import WinUserEnvDialog
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/utils/environ.py", line 17, in <module>
from spyderlib.widgets.dicteditor import DictEditor
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/widgets/dicteditor.py", line 28, in <module>
from spyderlib.utils.qthelpers import mimedata2url
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/utils/qthelpers.py", line 24, in <module>
from spyderlib.guiconfig import get_shortcut
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/guiconfig.py", line 24, in <module>
from spyderlib.widgets.sourcecode import syntaxhighlighters as sh
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/widgets/sourcecode/syntaxhighlighters.py", line 32, in <module>
required_version=PYGMENTS_REQVER)
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/dependencies.py", line 70, in add
installed_version)]
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/dependencies.py", line 32, in __init__
self.installed_version = programs.get_module_version(modname)
File "/home/daniel/anaconda3/lib/python3.4/site-packages/spyderlib/utils/programs.py", line 218, in get_module_version
mod = __import__(module_name)

File "/home/daniel/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Pygments-1.6-py2.7.egg/pygments/init.py", line 46 except TypeError, err: ^ SyntaxError: invalid syntax

I installed Conda 3.7 by downloading the .sh file through http://continuum.io/downloads#py34 and then installing it through the terminal with "bash Anaconda3-2.1.0-Linux-x86_64.sh"

What could be the issue?

I may have spotted the issue but still need some help:

When I first made this Ubuntu installation, I put QIIME on here (which is a suite of programs that have been made to work in their own environment for bioinformatics).

I see that in the list of file calls, everything is coming from .../anaconda3/... until the very last line, something is mistakenly (?) called from .../qiime_software/...

I'm assuming this is from both software suites containing python in their PATHs... how may this be fixed? Granted when I check "which python" in the terminal, it (correctly) outputs:

/home/daniel/anaconda3/bin/python

I almost thought a prior question asked here: Anaconda Spyder Qt library error on launch would lead me on the right path but I hit a deadend.

Update:

echo $PYTHONPATH spits out:

/home/daniel/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/lib/:/home/daniel/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages:/home/daniel/qiime_software/qiime-1.8.0-release/lib/:/home/daniel/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pprospector-1.0.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/tax2tree-1.0-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pynast-1.2.2-release/lib/python2.7/site-packages:/home/daniel/qiime_software/emperor-0.9.3-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages:/home/daniel/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/ipython-latest-repository-184467d4/lib/python2.7/site-packages:/home/daniel/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages:/home/daniel/qiime_software/mpi4py-1.2.2-release/lib/python2.7/site-packages:/home/daniel/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages:/home/daniel/qiime_software/gdata-2.0.17-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pysqlite-2.6.3-release/lib/python2.7/site-packages:/home/daniel/qiime_software/qcli-0.1.0-release/lib/python2.7/site-packages:/home/daniel/qiime_software/tornado-3.1.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/SQLAlchemy-0.7.1-release/lib/python2.7/site-packages:/home/daniel/qiime_software/pyzmq-2.1.11-release/lib/python2.7/site-packages:/home/daniel/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages:

Any help is appreciated.

Solution

Python looks up modules in the environment variable PYTHONPATH, so try echo $PYTHONPATH on the shell. Normally, this should be empty.

Otherwise you can try to run spyder from a dedicated environment, so try something like:

$ conda create -n spydertest spyder
$ source activate spydertest
$ spyder

Answered By - Wolfgang Ulmer