Linux – How to install python with proper permissions

linuxpythonroot

So python installed probably fine. Or perhaps it was already on here (I'm using xubuntu 12.10).

But I tried to install networkx today using pip:

pip install networkx

then says I don't have permission. So I sudo the above command. Installs without errors.

Now I can't import networkx without being root. I'm fairly confident you shouldn't have to be root all the time to run python scripts. That sounds really dangerous.

easy_install says this:

easy_install networkx

error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in
the installation directory:
[Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/test-easy-install-13206.pth'
The installation directory you specified (via –install-dir, –prefix,
or the distutils default setting) was:
/usr/local/lib/python2.7/dist-packages/
Perhaps your account does not have write access to this directory? If
the installation directory is a system-owned directory, you may need
to sign in as the administrator or "root" account. If you do not have
administrative access to this machine, you may wish to choose a
different installation directory, preferably one that is listed in
your PYTHONPATH environment variable.

For information on other options, you may wish to consult the
documentation at:

http://packages.python.org/distribute/easy_install.html

Please make the appropriate changes for your system and try again.

I also tried installing into ~/.networkx (a subfolder i created as not-root) and I get the same permissions error. I chmod 777 /usr/local/lib/python2.7/dist-packages and try to install, same permissions error.

pip uninstall and sudo easy_install causes the same problems as the pip install.

which by the way is:

python t1.py

Traceback (most recent call last): File "t1.py", line 3, in
import networkx as nx ImportError: No module named networkx

sudo python t1.py

H: 10
… more stuff that indicate its importing and working fine …

Clearly, I've just been a noob at some point in either installing python, or… anywhere else. I don't know where, it could be anywhere.
Has anyone encountered this before or is cluey enough to know what's going on? I need your halp. Cheers.

EDIT: (More info for Radoo)

sean@potatocake:~$./sh.sh
User is not part of the group which has access to that directory.
/usr/local/lib/python2.7/dist-packages needs access.

sean@potatocake:~$ll /usr/local/lib/
total 12
drwxrwxr-x 3 root root  4096 Mar 28 19:00 perl
drwxrwsr-x 4 root staff 4096 Oct 18 04:07 python2.7
drwxrwsr-x 3 root staff 4096 Oct 18 04:05 python3.2

sean@potatocake:~$ll /usr/local/lib/python2.7/
total 8
drwxrwsr-x 32 root staff 4096 Mar 28 23:13 dist-packages
drwxrwsr-x  2 root staff 4096 Oct 18 04:07 site-packages

note: I chmod'd this back to 775 when a non-sudo pip still didn't work.

sean@potatocake:~$groups
sean adm cdrom sudo dip plugdev lpadmin sambashare

sean@potatocake:~$sudo useradd -G staff sean
useradd: user 'sean' already exists

Best Answer

It's best not to try to override the system's version of Python. That version is there for the system. Customization to system's Python might cause conflicts or even open your system up to vulnerabilities. Also, system updates will probably revert your customization.

It's best to use your own version of Python, which can be done with tools such as virtualenv or pyenv.

Related Solutions

The suggested way to handle pip(easy_install) with homebrew

Maybe it is time to consider using virtualenv. Virtualenv creates self-contained python environments using the python version you specify. After activating the new virtual environment, everything you install using pip goes under that environment. This helps avoid situations like the one you described.

E.g. create and activate a new python environment using the default python:

# create environment
$ virtualenv --distribute myproject
New python executable in myproject/bin/python
Installing distribute...done.
Installing pip...done.

# activate environment
$ . ./myproject/bin/activate

# check default python
(myproject)$ which python
/Users/me/myproject/bin/python

It is suggested to use the --distribute options to indicate that distribute should be used for installing packages in the new environment instead of (the older) setuptools. After activation your command prompt changes to indicate which python environment is active.

Now install some package. The files will go into myproject directory:

# install django
(myproject)$ pip install django
...

# search for django dir
(myproject)$ find myproject -iname django
myproject/lib/python2.7/site-packages/django

Finally, deactivate:

# deactivate and check for default python
(myproject)$ deactivate
$ which python
/usr/bin/python

To create an environment using a non-default version of python:

$ virtualenv --distribute -p /path/to/custom/python mynewproject

By default virtualenv will copy to the new environment any packages installed for the python version you use to bootstrap it. To prevent this and create an empty environment use the --no-site-packages option. This is especially useful to create environments which can be exactly replicated e.g. from development to production.

Update: As of version 1.7 --no-site-packages has become the default behaviour of virtualenv.

If you want more details, there are plenty of tutorials and blog posts online. E.g.:

Notes on using pip and virtualenv with Django. (most of the post is not django-specific)
Working with virtualenv.

Give it a try and I'm sure you'll stick with it.

Note: Make sure that your executable scripts do not have the python interpreter hardcoded. I.e. their first line should be #!/usr/bin/env python and not something like #!/usr/bin/python.

Linux – Python error In linux

I had this exact error using CentOS 6.7 (Final) on a 64 bit system. I had to change two paths in order for python to work again. (Specifically gdb was giving me the same error you were getting.)

export PYTHONHOME=/usr/lib64/python2.6/
export PYTHONPATH=/usr/lib64/python2.6/

Other answers were saying to only modify one of those variables or use the non-64bit lib folder. But this was the only method that worked for me. Hopefully this can help someone else. In your case you might want to use the python2.7 folder however. But you can use python2.6 to get back to a working system at least.

Best Answer

Related Solutions

The suggested way to handle pip(easy_install) with homebrew

Linux – Python error In linux

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