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installation - Anaconda distribution Python error [DatabaseError: database disk image is malformed]


There seems to be something wrong with my Anaconda Python installation.


When I run Python through cmd it works and I can also run Python programs directly through cmd, and even import scipy, numpy, matplotlib etc.


However, when I try to run IPython with cmd command 'ipython', I get the error:


Traceback (most recent call last):
  File "C:\Users\User\Anaconda\Scripts\ipython-script.py", line 5, in 
    sys.exit(start_ipython())
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\__init__.py", line 120, in start_ipython
    return launch_new_instance(argv=argv, **kwargs)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\config\application.py", line 563, in launch_instance
    app.initialize(argv)
  File "", line 2, in initialize
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\config\application.py", line 92, in catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\terminal\ipapp.py", line 332, in initialize
    self.init_shell()
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\terminal\ipapp.py", line 348, in init_shell
    ipython_dir=self.ipython_dir, user_ns=self.user_ns)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\config\configurable.py", line 354, in instance
    inst = cls(*args, **kwargs)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\terminal\interactiveshell.py", line 328, in __init__
    **kwargs
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\core\interactiveshell.py", line 465, in __init__
    self.init_history()
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\core\interactiveshell.py", line 1521, in init_history
    self.history_manager = HistoryManager(shell=self, parent=self)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\core\history.py", line 498, in __init__
    self.new_session()
  File "", line 2, in new_session
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\core\history.py", line 68, in needs_sqlite
    return f(self, *a, **kw)
  File "C:\Users\User\Anaconda\lib\site-packages\IPython\core\history.py", line 516, in new_session
    NULL, "") """, (datetime.datetime.now(),))
DatabaseError: database disk image is malformed

If you suspect this is an IPython bug, please report it at:
    https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@scipy.org

You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.

Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
    c.Application.verbose_crash=True

I think the error is due to the DatabaseError: database disk image is malformed error, but am unsure of what this means.


Any advice?



Answer



The problem is a corrupted sqlite database. In this case the history.sqlite database.


Please have a look in your profile folder (or the path you have set in the configuration) if you can find a history.sqlite file.


If you can find it, make a backup first (just in case you might need it) and then create a new, empty file with the same name (history.sqlite).


Now try to run IPython again and you should be able to start it.


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