pip/python: normal site-packages is not writeable

Question

I have a new Macbook - a user installed it, and then I installed a new user (mine), granted admin privileges and deleted the old one. I am on OS Catalina.

Since the installation I've been having several permission problems. VSCode can't find Jupyter Notebook, pip installs packages at ~/Library/Python/3.7/site-packages .

When I do which python3 I get usr/bin/python3 . When I do pip3 install <package> I get: Defaulting to user installation because normal site-packages is not writeable And then it says it has already been installed, even though I can't access it when I do import <package> .

It's seems clear that this is a permission problem, pip can't install to the "base" python, and them python can't find what I've installed into ~/Library/Python/3.7/site-packages .

I've tried reinstalling the OS, but since I haven't done a clean install, it didn't change anything. What am I missing? How exactly can I fix permissions? Where do I want packages to be installed ( venv sure, but some packages I want global (like jupyter ).

Answer 1

As @TomdeGeus mentioned in the comments, this command works for me:

Python 3:

python3 -m pip install [package_name]

Python 2:

python -m pip install [package_name]

Answer 2

It's best to not use the system-provided Python directly. Leave that one alone since the OS can change it in undesired ways, as you experienced.

The best practice is to configure your own Python version(s) and manage them on a per-project basis using virtualenv (for Python 2) or venv (for Python 3). This eliminates all dependency on the system-provided Python version, and also isolates each project from other projects on the machine.

Each project can have a different Python point version if needed, and gets its own site_packages directory so pip-installed libraries can also have different versions by project. This approach is a major problem-avoider.

Answer 3

python3.7 -m pip install [package_name]

(you should use the version that you have, of course)

solved it for me.

The most voted answer python3 -m pip install [package_name] does not help me here.

In my case, this was caused by a conflict with the dominating 3.6 version that was also installed as a default. You might ask yourself why you have 3.6 on your system, you will most probably not use that version now. The reason is that 3.6 is used as an independent default python version for many package installers. Those installers do not want to check which individual version you use and whether that fits, they just use 3.6 as a default, if you like it or not.

Here is a proof by example --upgrade pip :

pip3 install --upgrade pip

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pip in /home/USERNAME/.local/lib/python3.6/site-packages (20.3.1)

python3 -m pip install --upgrade pip

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pip in /home/USERNAME/.local/lib/python3.6/site-packages (20.3.1)

python3.7 -m pip install --upgrade pip

Collecting pip
Cache entry deserialization failed, entry ignored
Using cached https://files.pythonhosted.org/packages/ab/11/2dc62c5263d9eb322f2f028f7b56cd9d096bb8988fcf82d65fa2e4057afe/pip-20.3.1-py2.py3-none-any.whl
Installing collected packages: pip Successfully installed pip-20.3.1

Answer 4

It occurs with me when I the virtual enviroment folder name was : venv .

in this case, It gives errors like :

No module pip

Default folder is unwritable

renaming the folder solve the proplem.

Answer 5

sudo pip install

Worked for me. But pip install is not recommended to be run with sudo. The issue I was facing on BIGSUR was, it was using system python. Once I Installed python 3.9 using

brew install python@3.9

Then pip worked fine

Answer 6

For readers in 2022 who thought themselves accidentally update system pip :

If you saw this info in your terminal output:

Defaulting to user installation because normal site-packages is not writeable

then you will be fine. Use the pip3 you just updated to run:

pyenv global system # since I use pyenv
pip3 uninstall pip # this one does the trick

Then you can check again pip3 --version will point to the original old (XCode/System-) pip . Eg (2022/2/28):

pip 20.2.3 from /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip (python 3.8)

Answer 7

For me, none of the suggestions worked so I had to delete the current virtual environment folder venv and recreate it using one of the following commands:

python -m venv venv
python3 -m venv venv

Check the source of pip on Ubuntu 20.04

which pip

returns the correct path

/home/myname/fullstack/person_api/venv/bin/pip

UPDATE

I presume that some might encounter this problem because they set python path as environmental variable like this in ~/.bashrc :

python=/path/to/python

which you should not be doing: Instead we could do:

py=python
PATH=/path/to/python:$PATH

I bumped into this issue specifically because of this!

Answer 8

Check on the command line "which python" to see if it is the value you expect. If you have a virtual environment activated, check /venv/bin/activate to see the value of VIRTUAL_ENV= and make sure it is the correct path. The path may be wrong if you renamed or moved the project. If the path is wrong, you can delete the venv and make a new one.

Answer 9

Had this same issue on a fresh install of Debian 9.12. Rebooting my server solved the issue.

Answer 10

in my case python3 -m pip install [package_name] did not solve that. in my case, it was a problem related to other processes occupying the directory. I restart Pycharm and close any other program that might occupy this folder, and reinstalled the package in site-packages directory successfully.

Answer 11

I'm using Anaconda on Ubuntu and had the same problem.I fixed it by the following steps:

deactivating current environment

conda deactivate

Then, the base environment activates. I deactivated the base conda environment too. To do so, I used conda deactivate again.

Finally, I activate my project environment directly (instead of activating from the base environment) by the following command. Afterward, I installed the intended package successfully and worked perfectly.

conda activate myenv
pip install somepackage

Answer 12

When this problem occurred to me I have tried all the mentioned approaches but they don't seem to work.

Instead, restarting Python language server in my VSCode did the job - my SimPy package is now found. On Mac it is Cmd+Shift+P and select "Python: Restart Language Server".

Answer 13

Try sudo pip install <package_name> .

for some reason, the user cannot modify the site-packages folder.

Answer 14

In my case on Linux, the ownership of the conda env directory had changed to another Linux user (long story), and so the the normal site-packages was not writeable due to a permissions issue.

The solution was to change ownership back to the user doing pip install .

Answer 15

I met exactly the same issue.

I just type sudo python3.8 -m pip install .... and the error disappeared.

If I remove the sudo , issue remains.

Answer 16

Had similar issue on Ubuntu 20.04.4 LTS in VirtualBox, but none of the suggestions here worked for me.

I was trying to install open3d in a venv and every time I was getting "Defaulting to user installation because normal site-packages is not writeable" which at first I didn't even noticed. open3d was always being installed in /usr/bin/python3 environment. I've restarted the VM but without luck, so I guess the problem was not just missing write access.

So in VS Code, which was using the venv, importing open3d was not possible. But testing from terminal from the activated venv with python3 -c "import open3d as o3d; print(o3d.__version__)" was working fine and that confused me totally. I even broke my system pip installation using sudo, see further below if you want to know how to fix it.

Anyhow, the solution to my problem was to explicitly point to the python3 file in the venv where I wanted to install the package:

venv/bin/python3 -m pip install open3d

---

So I was testing out everything and eventually installed with sudo: sudo pip3 install open3d . This of course didn't solved the problem and open3d was still missing in the venv. Even worse, I got the message:

"WARNING: You are using pip version 21.3.1; however, version 22.0.4 is available. You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command."

So I did it but with sudo, updating the system pip and then found out here that this is not good:

WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

Following an advice here, I tried to revert to original version, only then pip3 broke:

sudo pip3 uninstall pip
sudo pip3 --version
sudo: pip3: command not found

The apt package was still there:

sudo apt install python3-pip python3-pip is already the newest version (20.0.2-5ubuntu1.6).

So I had to reinstalled to fix the problem:

sudo apt-get remove python3-pip
sudo apt install python3-pip

Answer 17

Maybe you have python , python3 , pip or pip3 aliased. In that case pip might not work well anymore, as the alias isn't always available and so pip / pip3 might resolve python / python3 differently compared to in your terminal.

That could give rise to pip / pip3 trying to install in the system python, and that could give rise to your error.

Answer 18

I tried ever single recommendation described here. In every instance, I get the exact same result: SyntaxError: invalid syntax (<stdin>, line 1)

I'm not sure who designed the system like this, but it seems basically useless, based on my experience so far. Either create a system that works, or don't create anything at all.

Answer 19

For those running on a Pi, that accidentally installed pip as root. Just chown the lib folder to the pi user:

sudo chown -R pi:pi /usr/local/lib/python3.9/