Installed Python using Anaconda, kernel error starting ipython

Question

I installed the anaconda version of python, and changed the PATH to allow python command to work in terminal.

However when I type ipython, I get the following error.

Traceback (most recent call last):
  File "/Users/mrbighit/anaconda/bin/ipython", line 6, in <module>
    sys.exit(start_ipython())
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/__init__.py", line 120, in start_ipython
    return launch_new_instance(argv=argv, **kwargs)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 563, in launch_instance
    app.initialize(argv)
  File "<string>", line 2, in initialize
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 92, in catch_config_error
    return method(app, *args, **kwargs)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 332, in initialize
    self.init_shell()
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 348, in init_shell
    ipython_dir=self.ipython_dir, user_ns=self.user_ns)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/config/configurable.py", line 354, in instance
    inst = cls(*args, **kwargs)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/terminal/interactiveshell.py", line 328, in __init__
    **kwargs
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 465, in __init__
    self.init_history()
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 1521, in init_history
    self.history_manager = HistoryManager(shell=self, parent=self)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/core/history.py", line 498, in __init__
    self.new_session()
  File "<string>", line 2, in new_session
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/core/history.py", line 68, in needs_sqlite
    return f(self, *a, **kw)
  File "/Users/mrbighit/anaconda/lib/python2.7/site-packages/IPython/core/history.py", line 516, in new_session
    NULL, "") """, (datetime.datetime.now(),))
OperationalError: attempt to write a readonly database

Opening the ipython qtconsole also give kernel errors. I've made sure I have the right conda list packages.

I believe you sudo installed Anaconda into your home directory, which is why you are having these problems. You can safely get rid of the /Users/mrbighit/anaconda directory and install Anaconda as your normal user. — Burhan Khalid
– Burhan Khalid, Commented Aug 3, 2014 at 11:44
I used the bash command to install Anaconda, I didn't specify the install directory, just followed the site instructions. I didn't use the sudo install. Should I do the graphical installation and install it into a different directory? — hamm44
– hamm44, Commented Aug 3, 2014 at 12:23

Padraic Cunningham · Accepted Answer · 2014-08-03 11:40:03Z

2

Look for a .config/ipython/history.sqlite file on your system and change ownership with:

sudo chown ..., root somehow owns the file which is why you are seeing the error.

answered Aug 3, 2014 at 11:40

Padraic Cunningham

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4 Comments

hamm44 Over a year ago

Could you kindly explain how to change ownership in the terminal commands? I'm very new to mac.

Padraic Cunningham Over a year ago

have you found the history.sqlite file? It may also be in somewhere like .ipython/profile_default

hamm44 Over a year ago

I used the 'find /Users/mrbighit -name "history.sqlite"' command, then I used the 'sudo chown -v'.. and it worked.

Padraic Cunningham Over a year ago

Yes, find is very handy, I wonder how it happened it the first place?

Shuo · Accepted Answer · 2014-08-03 03:43:57Z

0

Open a normal python REPL, run:

from IPython.utils.path import locate_profile
locate_profile('default')

Check that you have the write permission on the folder

answered Aug 3, 2014 at 3:43

Shuo

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1 Comment

hamm44 Over a year ago

/Users/mrbighit/.ipython/profile_default' is the location and I was able to see that the folder has write permission. I tried sudo ipython and ipython loads without a problem, but using just ipython I get the error meessage.

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