How to correctly uninstall numpy on MacOSX?

Question

I'm on a Mac, and I installed numpy and sklearn in that order. Now, I'm faced with these errors that have already been mentioned on SO several times:

sklearn "numpy.dtype has the wrong size, try recompiling" in both pycharm and terminal

ValueError: numpy.dtype has the wrong size, try recompiling

ImportError in importing from sklearn: cannot import name check_build

So, I try to remediate this error by uninstalling numpy, and reinstalling a previous version.

1) sudo pip install --upgrade numpy..gives permission error

...OSError: [Errno 1] Operation not permitted: '/tmp/pip-OVY0Vq-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'...

2) I tried brew uninstall numpy, but import numpy still works even after a shell restart.

The only thing left I can think of is to manually delete all of the numpy files, which, on a Mac seeem to be found under sudo rm -rf /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy

....but even that gives me a permission error. what gives?

Solution 1

To solve this, I did the following: (note that it is not entirely clear to me which of these solved the problem, since I didn't test thoroughly).

1) Installed python at Python.org instead of Mac's stupid version

2) re-installed all of the modules like numpy, scipy, matplotlib, sklearn and ran this:hash -r python according to this source: Symbol not found: __PyCodecInfo_GetIncrementalDecoder, because it doesn't make python use the cached versions of the modules.

3) Then, I realized that I had this issue: https://github.com/scipy/scipy/issues/5093. To solve it, I had to make sure I installed the scipy module using python -m pip install scipy='0.15.0' instead of just pip install scipy='0.15.0', because this solved the issue based on this source: Can't load Python modules installed via pip from site-packages directory.

So, in conclusion it turns out there really is a big different between what is installed by pip, and what is imported when python is executed from the terminal. So, to ensure that you are using the pip to install the modules into a particular python, you can use python -m pip install <package name>.

Solution 2

I guess you are using MAC OS. I did a workaround to ignore the existing version of numpy (which MAC won't let you uninstall), and install an upgraded version.

Command :

pip install --upgrade --ignore-installed --install-option '--install-data=/usr/local' numpy

Worked fine for me.

Solution 3

I also getting this when I try to install pandas in MAC, but following command help me to get work around. Following command will ignore any previously installed version. Not sure it really fix issue behind though, but you can also have a try:

sudo pip install numpy --ignore-installed numpy

Solution 4

What works for my Mac OS 10.13.6 (High Sierra):

1. Just keep uninstalling numpy: $sudo -H pip uninstall numpy DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Uninstalling numpy-1.16.2: Would remove: /Library/Python/2.7/site-packages/numpy-1.16.2.dist-info/* /Library/Python/2.7/site-packages/numpy/* ... Proceed (y/n)? y Successfully uninstalled numpy-1.16.2 $sudo -H pip uninstall numpy DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Uninstalling numpy-1.14.2: Would remove: /Library/Python/2.7/site-packages/numpy-1.14.2.dist-info/* ... Proceed (y/n)? y Successfully uninstalled numpy-1.14.2

2. (re-) Install numpy with option: $ sudo -H pip install --ignore-installed numpy
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Collecting numpy Downloading https://files.pythonhosted.org/packages/bc/90/3e71b5392bd81d8559917ee38857bb2e4b92c88e87211a68e339127b86f5/numpy-1.16.2-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 (13.9MB) 100% |████████████████████████████████| 13.9MB 921kB/s Installing collected packages: numpy Successfully installed numpy-1.16.2

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Comments

[reticentroot]

I probably would just remove the files manually and then to avoid errors and potentially damaging your operating system you should install your packages inside a virtual environment. E.g docs.python-guide.org/en/latest/dev/virtualenvs

[makansij]

but, are those the correct files to remove?

[makansij]

even with sudo.....it won't let me remove them though!! Suggestions??

[reticentroot]

Sudo chmod 777 the_path_to_file then try rm again.. that should give you read write access to the file

[makansij]

Okay, I try sudo chmod 777 /System/Library/Frameworks/Python.framework/Versions/2.7/Ext‌​ras/lib/python/numpy and I get chmod: Unable to change file mode on /System/Library/Frameworks/Python.framework/Versions/2.7/Ext‌​ras/lib/python/numpy‌​: Operation not permitted. What gives?

[reticentroot]

Last thing I would try is to use the su command to become a super user. It is the highest privilege level, perhaps then you can rm or chmod.. if this is a mac you might also want to repair your disk permissions using disk utility. The newer operating systems removed that option but you can Google how to do that.

[makansij]

Am I the only one who thinks this shouldn't be that difficult!!!??

[reticentroot]

No you're not the only one. I've never had this problem. I use pip or git exclusively (I don't use brew for python) and I always use a virtualenv. Installing on to your machines copy of python isn't good practice for a number of reasons. Instead of using terminal to remove it try and manually dragging and dropping the installation into the trash can. The os will ask for a password and that should be it.

[reticentroot]

Just as a thought your operating system is fighting you hard on this one you may want to rethink how you're going about doing this. It could be that case that if you did remove it, you might damage you'd os in some way. I would locate the file manually, inside whatever container/ version of python you are using.

[Eric Leschinski]

Mac OSX has snatched the scepter of root from your fingers through bash. So you physically cannot delete those files no matter how much you want to. Only an operating system reinstall will nuke them, which only an Apple genius can do for you at cost of time and money. Enjoy your golden handcuffs lol.

[tgunr]

Sounds like you have run up against System Intregrity Protection (SIP) which will prevent you from doing changes on certain files and folders. It can be disabled. See stackoverflow.com/questions/30768087/…

[makansij]

pip upgrade is the same as pip uninstall and then pip install

[SinOfWrath]

which version of python are you running mac version or the brew one?,

[makansij]

How do I find out?

[SinOfWrath]

by default it's the mac version even if you've installed python using brew, you should try installing numpy skearn using pip or pip3, also for python2.7 and python3 you will have to install libraries separately

[SinOfWrath]

python -c or python3 -c for checking path of python you're using

[SinOfWrath]

Let us continue this discussion in chat.

[Tidhar Klein Orbach]

adding -ignore-installed also solved the issue for me on centos. thanks!

[Samuel Gómez]

I had to use: sudo pip install --upgrade --ignore-installed --install-option '--install-data=/usr/local' numpy and it worked for me

[rj487]

You save my day!