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installation error

asked 11 years ago

k1 gravatar image

updated 11 years ago

I tried to install sage from source and also from PPA on Ubuntu 12.10. Both of them finish the installation without any problem, but when I run sage I get the following error:

k1@Think1:~$ sagemath


| Sage Version 5.8, Release Date: 2013-03-15 | | Type "notebook()" for the browser-based notebook interface. | | Type "help()" for help. |


/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/utils/path.py:289: > UserWarning: IPython dir '/home/k1/.sage/ipython-0.12' is not a writable location, using a temp directory.

" using a temp directory."%ipdir)

Traceback (most recent call last):

File "/usr/lib/sagemath/local/bin/sage-ipython", line 14, in <module> app.initialize()

File "<string>", line 2, in initialize

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error

return method(app, args, *kwargs)

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py", line 313, in initialize

super(TerminalIPythonApp, self).initialize(argv)

File "<string>", line 2, in initialize

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error

return method(app, args, *kwargs)

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/core/application.py", line 333, in initialize

self.load_config_file()

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/sage/misc/interpreter.py", line 693, in load_config_file

get_ipython_dir(), 'sage').location

File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/core/profiledir.py", line 209, in find_profile_dir_by_name

raise ProfileDirError('Profile directory not found in paths: %s' % dirname) ProfileDirError: Profile directory not found in paths: profile_sage

If you suspect this is an IPython bug, please report it at: https://github.com/ipython/ipython/is... 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

But if I run it as root then it works fine. I have installed it all without root permission though. I thought it might be a permission problem and gave all the permissions for the files to the user k1, but still the problems exists.

So, I gained the permission to '/home/k1/.sage' and now it runs, but there are new errors:

[SageTerminalApp] Could not set security dir permissions to private.

[SageTerminalApp] Could not set pid dir permissions to private.

and I can't open the notebook().

the output of "ls -l /home/k1/ | grep .sage" is empty.

The output of "ls -l /home/k1/.sage" is :

total 28

drwsrwsrwt 2 k1 k1 4096 Mar 28 20:37 cache

drwsrwsrwt 2 k1 k1 4096 Mar 28 16:11 db

-rwxrwxrwt 1 k1 k1 0 Mar 29 17:39 gp-expect.log

-rwsrwsrwt 1 k1 k1 0 Mar 28 20:20 init.sage

drwsrwsrwt 3 root root 4096 Mar 29 17:39 ipython-0.12

drwsrwsrwt 2 k1 k1 4096 Mar 28 19:26 matplotlib-1.1.0

drwsrwsrwt 3 root ...

(more)
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Your error seems to be related to permissions. Can you be more explicit on the procedure you used for installation ? Moreover, can you copy/paste the output of the commands "ls -l /home/k1/ | grep .sage" and "ls -l /home/k1/.sage" ?

vdelecroix gravatar imagevdelecroix ( 11 years ago )

First I downloaded the sage package from the website and unzipped it and ran the make command. it was installed and worked fine with root, but not under the user k1. Then I deleted it and added the ppa to the sources and installed it from there, same problem.

k1 gravatar imagek1 ( 11 years ago )

I've added the output of those commands at the end of the main post.

k1 gravatar imagek1 ( 11 years ago )

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answered 11 years ago

vdelecroix gravatar image

updated 11 years ago

Hi,

As you can see with the output of ls, some of the directory within .sage are owned by root, namely ipython-0.12, sage_notebook.sagenb and tmp. I don't know how such a thing could happen ! You can change the permissions with the command

sudo chown k1:k1 -R .sage

The command chown is for modifying users, k1:k1 means that you change the user and the group to k1 and -R is for recursive.

After that, it may work.

Vincent

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That worked just as you said. Thank you very much.

k1 gravatar imagek1 ( 11 years ago )

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Asked: 11 years ago

Seen: 1,221 times

Last updated: Mar 30 '13