OSX El Capitan: sudo pip install OSError: [Errno: 1] Operation not permitted

Question

When I run:

sudo pip install ipython

I get the following error

OSError: [Errno: 1] Operation not permitted: '/System/Library/Frameworks/Python.framework/Versions/2.7/share'

The last command executed tries to create the directory given above.

Also, the following command fails to install iPython without providing any errors.

sudo pip install --user python

(I am on Mac OS X El Capitan in case other folks on this OS see the same issue.)

Answer 1

Instructions telling sudo pip install are inherently wrong.

If there is any tutorial out there which says you should do sudo pip then please file a bug against this package. The author is dis-educating Python community, as time has proven sudo pip to be a broken practice.

OSX El Capitan introduced a mechanisms to prevent damaging the operating system files. /System/Library/Frameworks/Python.framework/Versions/2.7/share is one of the protected locations. A normal user has no reason to put or write any files there. This is because the operating system itself relies on these files and sudo pip, with all force given from the above, would unconditionally overwrite them. Usually bad things would not happen, but the chances are there. Apple wants to protect their OS users to accidentally bricking their installation.

Instead, you need to install a Python package, like IPython, locally to the home folder of your user. The easiest way is to create a virtual environment, activate it and then run pip in the virtual environment.

Example:

cd ~  # Go to home directory
virtualenv my-venv
source my-venv/bin/activate
pip install IPython

More info

• Official Python package installation tutorial.

• How to create virtual environments.

Alternatively, one should be able to do pip install --user. But again, no sudo needed and you need to manually set up PATH environment variable.

Answer 2

I had the same problems, but using easy_install "module" solved the problem for me.

I am not sure why, but pip and easy_install use different install locations, and easy_install chose the right ones.

Edit: without re-checking but because of the comments; it seems that different (OSX and brew-installed) installations interfere with each other which is why they tools mentioned indeed point to different locations (since they belong to different installations). I understand that usually those tools from one install point to the same folder.

Answer 3

You should reinstall Python:

brew reinstall python

To get brew see the brew homepage.

Answer 4

pip install --ignore-installed six

This will do the job, then you can try your first command.

Via http://github.com/pypa/pip/issues/3165

Answer 5

Used pip3 install <package> instead and solved the permission problem with pip.

Answer 6

I had the same issues. As others have mentioned, don't run pip install with sudo. Run

brew doctor 

and fix the warnings and you should be able to proceed with your pip install.

Answer 7

Same error

Installing collected packages: six, pyparsing, packaging, appdirs, setuptools
Exception:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py", line 851, in install
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py", line 1064, in move_wheel_files
    isolated=self.isolated,
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/wheel.py", line 345, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/wheel.py", line 323, in clobber
    shutil.copyfile(srcfile, destfile)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/six.py'

and here I use --user without sudo to solve this issue

$ pip install --user scikit-image h5py keras pygame
Collecting scikit-image
  Downloading http://mirrors.aliyun.com/pypi/packages/65/69/27a1d55ce8f77c8ac757938707105b1070ff4f2ae47d2dc99461bfae4491/scikit_image-0.13.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (28.1MB)
    100% |████████████████████████████████| 28.1MB 380kB/s
Collecting h5py
  Downloading http://mirrors.aliyun.com/pypi/packages/b7/cc/1c29b0815b12de2c92b5323cad60f724ac8f0e39d0166d0b9dfacbcb70dd/h5py-2.7.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.5MB)
    100% |████████████████████████████████| 4.5MB 503kB/s
Requirement already satisfied: keras in /Library/Python/2.7/site-packages
Requirement already satisfied: pygame in /Library/Python/2.7/site-packages
Requirement already satisfied: matplotlib>=1.3.1 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from scikit-image)
Requirement already satisfied: six>=1.7.3 in /Library/Python/2.7/site-packages (from scikit-image)
Requirement already satisfied: pillow>=2.1.0 in /Library/Python/2.7/site-packages (from scikit-image)
Requirement already satisfied: networkx>=1.8 in /Library/Python/2.7/site-packages (from scikit-image)
Requirement already satisfied: PyWavelets>=0.4.0 in /Library/Python/2.7/site-packages (from scikit-image)
Collecting scipy>=0.17.0 (from scikit-image)
  Downloading http://mirrors.aliyun.com/pypi/packages/72/eb/d398b9f63ee936575edc62520477d6c2353ed013bacd656bd0c8bc1d0fa7/scipy-0.19.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.2MB)
    100% |████████████████████████████████| 16.2MB 990kB/s
Requirement already satisfied: numpy>=1.7 in /Library/Python/2.7/site-packages (from h5py)
Requirement already satisfied: theano in /Library/Python/2.7/site-packages (from keras)
Requirement already satisfied: pyyaml in /Library/Python/2.7/site-packages (from keras)
Requirement already satisfied: python-dateutil in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: tornado in /Library/Python/2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: pyparsing>=1.5.6 in /Users/qiuwei/Library/Python/2.7/lib/python/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: nose in /Library/Python/2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: olefile in /Library/Python/2.7/site-packages (from pillow>=2.1.0->scikit-image)
Requirement already satisfied: decorator>=3.4.0 in /Library/Python/2.7/site-packages (from networkx>=1.8->scikit-image)
Requirement already satisfied: singledispatch in /Library/Python/2.7/site-packages (from tornado->matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: certifi in /Library/Python/2.7/site-packages (from tornado->matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: backports_abc>=0.4 in /Library/Python/2.7/site-packages (from tornado->matplotlib>=1.3.1->scikit-image)
Installing collected packages: scipy, scikit-image, h5py
Successfully installed h5py-2.7.0 scikit-image-0.13.0 scipy-0.19.0 

Hope it will help someone who encounter similar issue!

Answer 8

TL;DR $PATH fix

1. Use pip install --user package_name to install a package that should include CLI executables.
2. Launch a python shell and import package_name
3. Find where lib/python/... occurs in the output and replace it all with bin
4. It's likely to be $HOME/Library/Python/2.7/bin

Details

Because of the new System Integrity Protection in macOS 10.11 El Capitan, you can no longer sudo pip install. We won't debate the merits of that here.

Another answer explains that you should pip install --user which is correct. But they sent you to the back alleys to figure out what to do about your $PATH so that you could get access to installed executables. Luckily, I've already solved a similar need for an unrelated question.

Here is a transcript of how I solved the problem on one of my systems. I'm including it all rather just than the $PATH that worked for me, because your system may be different from mine. This process should work for everybody.

$ pip install --user jp
Collecting jp
  Downloading jp-0.2.4.tar.gz
Installing collected packages: jp
  Running setup.py install for jp ... done
Successfully installed jp-0.2.4

$ python -c 'import jp; print jp'
<module 'jp' from '/Users/bbronosky/Library/Python/2.7/lib/python/site-packages/jp/__init__.pyc'>

$ find /Users/bbronosky/Library/Python -type f -perm -100
/Users/bbronosky/Library/Python/2.7/bin/jp

$ which jp

$ echo -e '\n''export PATH=$HOME/Library/Python/2.7/bin:$PATH' >> ~/.bashrc

$ bash # starting a new bash process for demo, but you should open a new terminal

$ which jp
/Users/bbronosky/Library/Python/2.7/bin/jp

$ jp
usage: jp <expression> <filepath>

Answer 9

It is hard to get pip working on El Capitan for several reasons:

1. OS X doesn't set some distutils variables correctly, so pip tries to install ancillary files in locations under /System/Library/. El Capitan blocks this, which is the error you are running into.
2. OS X includes a number of outdated packages under /System/Library/. pip often wants to upgrade these but cannot on El Capitan.
3. OS X places /System/Library/ higher in the python search order than /Library/Python/2.7/site-packages (the system-wide python package location), so even if you manage to install newer versions of some packages, the old ones still get loaded, breaking some dependencies.

There are workarounds for all of these at https://apple.stackexchange.com/a/223163/143849 . But you may be best off installing your own version of Python via the standard Python installer, Homebrew or Anaconda.

Answer 10

I guess you have some conflict with other package. For me it was six. So you need to use a command like this:

pip install google-api-python-client --upgrade --ignore-installed six

or

pip install --ignore-installed six

Answer 11

I fully agree with Mikko, but if you still want to do it, here is the way:

• Restart in recovery mode (Hold cmd + R)
• Open terminal from utilities
• Use the command csrutil disable

Answer 12

I have python2.7 installed via brew and the following solved my problem

brew install numpy

It installs python3, but it still works and sets it up for 2.7 as well.

Answer 13

Like you I had the same problem. I'm running El Capitan and trying to install Juypter with python2.7 Here's how I was able to do it:

First install Juypter (would work also with pip3):

sudo -H pip install --ignore-installed six --user --install jupiter

Then you need install the python 2.7 kernel, otherwise you'll only be able to use python3 for the notebook.

sudo -H python -m pip install --user --ignore-installed six --upgrade ipykernel
python -m ipykernel install --user

This may be useful for those who wish to keep the Apple installation of python2.7 and want to use the Jupyter notebook with both python2.7 and python3.

Answer 14

This did it for me after pip install ipython failed:

SF55M:~ 278$ sudo easy_install ipython
Searching for ipython
Best match: ipython 5.4.1
Adding ipython 5.4.1 to easy-install.pth file
Installing ipython script to /usr/local/bin
Installing iptest2 script to /usr/local/bin
Installing iptest script to /usr/local/bin
Installing ipython2 script to /usr/local/bin

Using /Library/Python/2.7/site-packages
Processing dependencies for ipython
Finished processing dependencies for ipython
SF55M:~ 278$ pip install ipython
Requirement already satisfied: ipython in /Library/Python/2.7/site-packages
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in 
/Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: decorator in /Library/Python/2.7/site-
packages (from ipython)
Requirement already satisfied: setuptools>=18.5 in /Library/Python/2.7/site-
packages/setuptools-19.6.1-py2.7.egg (from ipython)
Requirement already satisfied: pickleshare in /Library/Python/2.7/site-
packages (from ipython)
Requirement already satisfied: pygments in /Library/Python/2.7/site-packages 
(from ipython)
Requirement already satisfied: pexpect; sys_platform != "win32" in 
/Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: pathlib2; python_version == "2.7" or 
python_version == "3.3" in /Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: backports.shutil-get-terminal-size; 
python_version == "2.7" in /Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: simplegeneric>0.8 in 
/Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: traitlets>=4.2 in /Library/Python/2.7/site-
packages (from ipython)
Requirement already satisfied: appnope; sys_platform == "darwin" in 
/Library/Python/2.7/site-packages (from ipython)
Requirement already satisfied: six>=1.9.0 in /Library/Python/2.7/site-
packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython)
Requirement already satisfied: wcwidth in /Library/Python/2.7/site-packages 
(from prompt-toolkit<2.0.0,>=1.0.4->ipython)
Requirement already satisfied: ptyprocess>=0.5 in /Library/Python/2.7/site-
packages (from pexpect; sys_platform != "win32"->ipython)
Requirement already satisfied: scandir; python_version < "3.5" in 
/Library/Python/2.7/site-packages (from pathlib2; python_version == "2.7" or 
python_version == "3.3"->ipython)
Requirement already satisfied: enum34; python_version == "2.7" in 
/Library/Python/2.7/site-packages (from traitlets>=4.2->ipython)
Requirement already satisfied: ipython-genutils in /Library/Python/2.7/site-
packages (from traitlets>=4.2->ipython)
SF55M:~ 212580378$ ipython
Python 2.7.10 (default, Feb  7 2017, 00:08:15)
Type "copyright", "credits" or "license" for more information.

IPython 5.4.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:
Do you really want to exit ([y]/n)?
SF55M:~ 278$

Answer 15

It worked for me as I have python 2 & 3 both are installed.

brew reinstall python@2

Answer 16

I just installed it using easy_install

Eg: $ sudo easy_install networkx