Why is pip, inside a virtualenv, writing to /usr/lib?

Question

I'm running Python on a slightly older OS, whose system Python is at version 2.6. Hence I have 2.7 installed in my home directory and used that Python to get pip, and used that pip to install virtualenvwrapper. So I have

$ which python pip virtualenv virtualenvwrapper.sh
/home/user/bin/python
/home/user/bin/pip
/home/user/.local/bin/virtualenv
/home/user/.local/bin/virtualenvwrapper.sh

I use these tools to create a virtualenv, and try to install a module

$ mkvirtualenv fred
New python executable in fred/bin/python2.7.10
Also creating executable in fred/bin/python
Installing setuptools, pip, wheel...done.
virtualenvwrapper.user_scripts creating /home/user/.virtualenvs/fred/bin/predeactivate
virtualenvwrapper.user_scripts creating /home/user/.virtualenvs/fred/bin/postdeactivate
virtualenvwrapper.user_scripts creating /home/user/.virtualenvs/fred/bin/preactivate
virtualenvwrapper.user_scripts creating /home/user/.virtualenvs/fred/bin/postactivate
virtualenvwrapper.user_scripts creating /home/user/.virtualenvs/fred/bin/get_env_details

$ workon fred
$ export PYTHONPATH=/home/user/.virtualenvs/fred/lib/python2.7/site-packages
$ /home/user/.virtualenvs/fred/bin/easy_install --prefix=/home/user/.virtualenvs/fred pip
Creating /home/user/.virtualenvs/fred/lib/python2.7/site-packages/site.py
Searching for pip
Best match: pip 7.1.2
Adding pip 7.1.2 to easy-install.pth file
Installing pip script to /home/user/.virtualenvs/fred/bin
Installing pip3.4 script to /home/user/.virtualenvs/fred/bin
Installing pip3 script to /home/user/.virtualenvs/fred/bin

Using /home/user/.virtualenvs/fred/lib/python2.7/site-packages                                                                                                           
Processing dependencies for pip
Finished processing dependencies for pip

$ which python pip 
/home/user/.virtualenvs/fred/bin/python
/home/user/.virtualenvs/fred/bin/pip

$ pip install itsdangerous
Collecting itsdangerous
Installing collected packages: itsdangerous

Exception:
Traceback (most recent call last):
  File "/home/user/.local/lib/python2.7/site-packages/pip/basecommand.py", line 211, in main
    status = self.run(options, args)
  File "/home/user/.local/lib/python2.7/site-packages/pip/commands/install.py", line 311, in run
    root=options.root_path,
  File "/home/user/.local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install
    **kwargs
  File "/home/user/.local/lib/python2.7/site-packages/pip/req/req_install.py", line 803, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/home/user/.local/lib/python2.7/site-packages/pip/req/req_install.py", line 998, in move_wheel_files
    isolated=self.isolated,
  File "/home/user/.local/lib/python2.7/site-packages/pip/wheel.py", line 341, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/home/user/.local/lib/python2.7/site-packages/pip/wheel.py", line 319, in clobber
    shutil.copyfile(srcfile, destfile)
  File "/usr/lib64/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/usr/lib/python2.7/site-packages/itsdangerous.py'

Why is pip trying to install the module into /usr/lib? Shouldn't it be installed to ~/.virtualenvs/fred/lib, or ~/lib?

Status as of Jul 4th, 2018: Unreproducible, as I do not have access to that company's servers any more, and I have not seen it on other systems since.

Answer 1

Probably your are calling the system level pip and not the virtualenv pip.

You should activate your virtualenv before:

. bin/activate