"OSError: [Errno 1] Operation not permitted" when installing Scrapy in OSX 10.11 (El Capitan) (System Integrity Protection)

Question

I'm trying to install Scrapy Python framework in OSX 10.11 (El Capitan) via pip. The installation script downloads the required modules and at some point returns the following error:

OSError: [Errno 1] Operation not permitted: '/tmp/pip-nIfswi-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six-1.4.1-py2.7.egg-info'

I've tried to deactivate the rootless feature in OSX 10.11 with the command:

sudo nvram boot-args="rootless=0";sudo reboot

but I still get the same error when the machine reboots.

Any clue or idea from my fellow StackExchangers?

If it helps, the full script output is the following:

sudo -s pip install scrapy
Collecting scrapy
  Downloading Scrapy-1.0.2-py2-none-any.whl (290kB)
    100% |████████████████████████████████| 290kB 345kB/s 
Requirement already satisfied (use --upgrade to upgrade): cssselect>=0.9 in /Library/Python/2.7/site-packages (from scrapy)
Requirement already satisfied (use --upgrade to upgrade): queuelib in /Library/Python/2.7/site-packages (from scrapy)
Requirement already satisfied (use --upgrade to upgrade): pyOpenSSL in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from scrapy)
Collecting w3lib>=1.8.0 (from scrapy)
  Downloading w3lib-1.12.0-py2.py3-none-any.whl
Collecting lxml (from scrapy)
  Downloading lxml-3.4.4.tar.gz (3.5MB)
    100% |████████████████████████████████| 3.5MB 112kB/s 
Collecting Twisted>=10.0.0 (from scrapy)
  Downloading Twisted-15.3.0.tar.bz2 (4.4MB)
    100% |████████████████████████████████| 4.4MB 94kB/s 
Collecting six>=1.5.2 (from scrapy)
  Downloading six-1.9.0-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): zope.interface>=3.6.0 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from Twisted>=10.0.0->scrapy)
Requirement already satisfied (use --upgrade to upgrade): setuptools in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from zope.interface>=3.6.0->Twisted>=10.0.0->scrapy)
Installing collected packages: six, w3lib, lxml, Twisted, scrapy
  Found existing installation: six 1.4.1
    DEPRECATION: Uninstalling a distutils installed project (six) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
    Uninstalling six-1.4.1:
Exception:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/basecommand.py", line 223, in main
status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/commands/install.py", line 299, in run
root=options.root_path,
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/req/req_set.py", line 640, in install
requirement.uninstall(auto_confirm=True)
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/req/req_install.py", line 726, in uninstall
paths_to_remove.remove(auto_confirm)
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/req/req_uninstall.py", line 125, in remove
renames(path, new_path)
  File "/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg/pip/utils/__init__.py", line 314, in renames
shutil.move(old, new)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move
copy2(src, real_dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2
copystat(src, dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat
os.chflags(dst, st.st_flags)
OSError: [Errno 1] Operation not permitted: '/tmp/pip-nIfswi-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six-1.4.1-py2.7.egg-info'

Solution 1

I also think it's absolutely not necessary to start hacking OS X.

I was able to solve it doing a

brew install python

It seems that using the python / pip that comes with new El Capitan has some issues.

Solution 2

pip install --ignore-installed six

Would do the trick.

Source: github.com/pypa/pip/issues/3165

Solution 3

As the other answers said, it's because of the new System Integrity Protection, but I believe the other answers are overcomplicated.

If you're only gonna use that package in the current user, you should be able to install it just fine, without the need to disable the SIP, by using the --user flag. Like this:

sudo pip install --user packagename

Solution 4

The high voted answers didn't work for me, it seems to work for El Capitan users. But for MacOS Sierra users try the following steps

1. brew install python
2. sudo pip install --user <package name>

Solution 5

Warnings

I would suggest very strongly against modifying the system Python on Mac; there are numerous issues that can occur.

Your particular error shows that the installer has issues resolving the dependencies for Scrapy without impacting the current Python installation. The system uses Python for a number of essential tasks, so it's important to keep the system installation stable and as originally installed by Apple.

I would also exhaust all other possibilities before bypassing built in security.

Package Manager Solutions:

Please look into a Python virtualization tool such as virtualenv first; this will allow you to experiment safely.

Another useful tool to use languages and software without conflicting with your Mac OS is Homebrew. Like MacPorts or Fink, Homebrew is a package manager for Mac, and is useful for safely trying lots of other languages and tools.

"Roll your own" Software Installs:

If you don't like the package manager approach, you could use the /usr/local path or create an /opt/local directory for installing an alternate Python installation and fix up your paths in your .bashrc. Note that you'll have to enable root for these solutions.

How to do it anyway:

If you absolutely must disable the security check (and I sincerely hope it's for something other than messing with the system languages and resources), you can disable it temporarily and re-enable it using some of the techniques in this post on how to Disable System Integrity-Protection.

View more solutions

Comments

[hectorpal]

Possible duplicate of Unable to install nltk on Mac OS El Capitan

[hectorpal]

The questions is being discussed here: apple.stackexchange.com/questions/209572/…

[nvg58]

Maybe you it helps you without disable SIP: stackoverflow.com/a/32930419/3090526

[Arabasta]

I had the exact same problem when I tried installing "virtualenvwrapper" using pip but this command worked for me: "sudo pip install --ignore-installed virtualenvwrapper" So it might be apply to your case as well without having to go through a painful round-about

[rholmes]

It's a bit of an investment in time and requires some command line proficiency, but the result is well worth it - I use similar virtual environments for Ruby (RVM), Perl, etc. Homebrew is useful for safely trying lots of other languages and tools as well.

[Sacrilicious]

no, no, no. This is a util running in user space. Please see stackoverflow.com/a/33024464/743638 for a relatively simple way around this. Disabling protection from 1. unsigned kernel extensions 2. modify systems binaries 3. inspecting and mounting over system paths etc. etc. is just foolhardy. At least recommend TEMPORARILY removing SIP until after install, and then turning it back on.

[Mario]

I would not do this. This is asking for trouble. For a more graceful solution approach see my answer below.

[Ergun Ozyurt]

the question was unanswered more than a month. i think, this was the only "findable" solution at that time. i will edit my answer with some warning to enable SIP after everyting has been installed.

[Luke]

This worked well for me when installing awscli on El Capitan without messing with the python installation: sudo pip install --ignore-installed awscli

[harinsa]

couldn't import scrapy when installed with this method ImportError: cannot import name xmlrpc_client

[Friendly King]

--ignore-installed flag did the trick for the AWS Elastic Beanstalk Cli for me as well. Finally...

[Paul Carlton]

this worked well for me as well. I think this should be the correct answer.

[Verticon]

This worked for me. Thank you for saving me from going into the OS tweaks snake pit!

[Russell_A]

Worked for me too, and got me the next Python 2.7.X. This answer should win

[Sophia Feng]

This worked for me in sudo pip install --ignore-installed scrapy.

[Translunar]

This didn't work for me for Numpy/Matplotlib. I'm trying to upgrade Matplotlib, but can't seem to uninstall Numpy 1.8.0rc1 and replace it with Numpy 1.11.0.

[olleh]

still needs sudo tho!

[dmgig]

Worked for me installing TensorFlow

[loretoparisi]

Amazing, this finally solved my problem on El Capitan! My temporary solution was to use virtualenv that worked as well, but for a specific environment I needed packages on whole system to be installed. Now it worked like a charm: sudo pip install --ignore-installed --upgrade -r requirements.txt

[zzzzzzzzzzzzzzzzzzzzzzzzzzzzzz]

This is the best answer for El Capitan Mac users

[Ramesh Ramasubramanian]

@Luke I had the same issue yesterday when I tried to install the latest version of numpy. Your suggestion worked and saved me all kinds of time. Thank you.

[xdhmoore]

I'm unclear on precisely how these different flags work, but this answer seems to make the most sense to me. (Also, it worked :)

[dietbacon]

@xdhmoore Thanks, I think so too haha. No need to disable SIP or to install a new python or mess with dependencies.

[Muaaz salagar]

You have pointed it out correctly ! This should be accepted answer!

[Rob]

For mkvirtualenv, this did not install the package in the expected location /usr/local/bin. Instead, sudo pip install mkvirtualenv --ignore-installed six works as expected, putting virtualenvwrapper.sh in /usr/local/bin

[Rob]

Yes, this works for sudo pip install virtualenvwrapper --ignore-installed six as well, avoiding this error: OSError: [Errno 1] Operation not permitted: '/tmp/..../System/Library/Frameworks/Python.framework/Versio‌​ns/2.7/Extras/lib/py‌​thon/six-1.4.1-py2.7‌​.egg-info'

[dietbacon]

@Rob It really doesn't. The --user flag only installs for current user, so it makes sense that it wouldn't install in a folder that is not user-specific. For me, this command installs my packages in "/Users/myusername/Library/Python/2.7/lib/python/site-packag‌​‌​es" for .py files and "/Users/myusername/Library/Python/2.7/bin" for .sh files

[Rob]

@dietbacon I think we are in agreement? The command I shared put it in a system-wide available location, yours is for installing it for a given user.

[dietbacon]

@Rob Yeah, sort of. But /usr/local/bin shouldn't be the expected location if you're installing something only for the current user, as I wrote that was the case in the answer.

[Timothy Swan]

This appeared to install in the user space for me, but then wasn't linked. What is the step to make sure that it is linked? OS X El Capitan 10.11.6

[dietbacon]

@TimothySwan That's weird. If it's in "/Users/myusername/Library/Python/2.7/lib/python/site-packag‌​‌​‌​es" or "/Users/myusername/Library/Python/2.7/bin", python should find it automatically, unless you're using another version of python you manually installed I think. You can see where python is loading packages from by opening the python shell, then running import sys and sys.path. That should show you the folders where python is looking for packages.

[QADeveloper]

This worked for me.. i think this is a better solution

[Datageek]

sudo pip install --user <package name> worked for me, without the need to reinstall the python

[HibernatedGuy]

worked for me. I faced the same issue while I was installing virtualenvwrapper on HighSierra.

[nantitv]

This worked for me for a rasa-nlu . sudo pip install --user rasa_nlu

[Michael Guild]

that did it for me. ( Sierra 10.13.6 )

[Mario]

@codersofthedark maybe brew install python3 could solve this as on newer systems python3 is now the default python.

[Thomas Crawford]

Worked for me as well.