pip installing in global site-packages instead of virtualenv

Using pip3 to install a package in a virtualenv causes the package to be installed in the global site-packages folder instead of the one in the virtualenv folder. Here's how I set up Python3 and virtualenv on OS X Mavericks (10.9.1):

I installed Python3 using Homebrew:

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew install python3 --with-brewed-openssl

Changed the $PATH variable in .bash_profile; added the following line:

export PATH=/usr/local/bin:$PATH

Running which python3 returns /usr/local/bin/python3 (after restarting the shell).

Note: which python3 still returns /usr/bin/python though.

Installed virtualenv using pip3:

pip3 install virtualenv

Next, create a new virtualenv and activate it:

virtualenv testpy3 -p python3
cd testpy3
source bin/activate

Note: if I don't specify -p python3, pip will be missing from the bin folder in the virtualenv.

Running which pip and which pip3 both return the virtualenv folder:

/Users/kristof/VirtualEnvs/testpy3/bin/pip3

Now, when I try to install e.g. Markdown using pip in the activated virtualenv, pip will install in the global site-packages folder instead of the site-packages folder of the virtualenv.

pip install markdown

Running pip list returns:

Markdown (2.3.1)
pip (1.4.1)
setuptools (2.0.1)
virtualenv (1.11)

Contents of /Users/kristof/VirtualEnvs/testpy3/lib/python3.3/site-packages:

__pycache__/
_markerlib/
easy_install.py
pip/
pip-1.5.dist-info/
pkg_resources.py
setuptools/
setuptools-2.0.2.dist-info/

Contents of /usr/local/lib/python3.3/site-packages:

Markdown-2.3.1-py3.3.egg-info/
__pycache__/
easy-install.pth
markdown/
pip-1.4.1-py3.3.egg/
setuptools-2.0.1-py3.3.egg
setuptools.pth
virtualenv-1.11-py3.3.egg-info/
virtualenv.py
virtualenv_support/

As you can see, the global site-packages folder contains Markdown, the virtualenv folder doesn't.

Note: I had Python2 and Python3 installed before on a different VM (followed these instructions) and had the same issue with Python3; installing packages in a Python2 based virtualenv worked flawlessly though.

Any tips, hints, … would be very much appreciated.

Funny you brought this up, I just had the exact same problem. I solved it eventually, but I'm still unsure as to what caused it.

Try checking your bin/pip and bin/activate scripts. In bin/pip, look at the shebang. Is it correct? If not, correct it. Then on line ~42 in your bin/activate, check to see if your virtualenv path is right. It'll look something like this

VIRTUAL_ENV="/Users/me/path/to/virtual/environment"

If it's wrong, correct it, deactivate, then . bin/activate, and if our mutual problem had the same cause, it should work. If it still doesn't, you're on the right track, anyway. I went through the same problem solving routine as you did, which piping over and over, following the stack trace, etc.

Make absolutely sure that

/Users/kristof/VirtualEnvs/testpy3/bin/pip3

is what you want, and not referring to another similarly-named test project (I had that problem, and have no idea how it started. My suspicion is running multiple virtualenvs at the same time).

If none of this works, a temporary solution may be to, as Joe Holloway said,

> Just run the virtualenv's pip with its full path (i.e. don't rely on searching the executable path) and you don't even need to activate the environment. It will do the right thing.

Perhaps not ideal, but it ought to work in a pinch.

Link to my original question:

https://stackoverflow.com/questions/20942982/virtualenv-pip-trying-to-install-packages-globally

For me this was not a pip or virtualenv problem. It was a python problem. I had set my $PYTHONPATH manually in ~/.bash_profile (or ~/.bashrc) after following some tutorial online. This manually set $PYTHONPATH was available in the virtualenv as it probably should be allowed.

Additionally add2virtualenv was not adding my project path to my $PYTHONPATH for some reason within the virtualenv.

Just some forking paths for those who might still be stuck! Cheers!

I had the same problem, I solved it by removing venv directory and recreating it!

deactivate (if venv is activated first deactivate it)
rm -rf venv
virtualenv -p python3 venv
. ENV/bin/activate
pip3 install -r requirements.txt

Now everything works like a charm.

I had the same issue on macos with python 2 and 3 installed.

Also, I had aliases to point to python3 and pip3 in my .bash_profile.

alias python=/usr/local/bin/python3
alias pip=/usr/local/bin/pip3

Removing aliases and recreating virtual env using python3 -m venv venv fixed the issue.

The first thing to check is which location pip is resolving to:

which pip

if you are in a virtualenv you would expect this to give you something like:

> /path/to/virtualenv/.name_of_virtualenv/bin/pip

However it may be the case that it's resolving to your system pip for some reason. For example you may see this from within your virtualenv (this is bad):

> /usr/local/bin/pip (or anything that isn't in your virtualenv path).

To solve this check your pipconfig in:

~/.pipconf
~/.conf/pip
/etc/pip.conf

and make sure that there is nothing that is coercing your Python path or your pip path (this fixed it for me).

Then try starting a new terminal and rebuild your virtualenv (delete then create it again)

Go to bin directory in your virtual environment and write like this:

./pip3 install <package-name>

I had this problem too. Calling pip install <package_name> from the /bin directory within my Python 3.3 virtual environment on my Mavericks Mac caused the Python package to be installed in the Python 2.7 global site packages directory. This was despite the fact that my $PATH started with the directory containing pip. Weird. This doesn't happen on CentOS. For me, the solution was calling pip3 instead of pip. When I had installed pip within the virtual environment via ez_setup, three "pip" executables had been installed in the /bin directory - pip, pip3, and pip3.3. Curiously, all three files were exactly the same. Calling pip3 install <package_name> caused the Python package to be installed correctly into the local site-packages directory. Calling pip with the full pathname into the virtual environment also worked correctly. I'd be interested to know why my Mac isn't using $PATH the way I would expect it to.

I hit into the same issue while installing a python package from within a virtualenv. The root cause in my case was different. From within the virtualenv, I was (out of habit on Ubuntu), doing:

sudo easy_install -Z <package>

This caused the bin/pip shebang to be ignored and it used the root's non virtualenv python to install it in the global site-packages. Since we have a virtual environment, we should install the package without "sudo"

I stumbled upon the same problem running Manjaro. I created the virtual environment using python3 -m ven venv and then activated using source venv/bin/actiave. which python and which pip both pointed towards the correct binaries in the virtualenv, however I was not able to install to the virtualenv, even when using the full path of the binaries. Turned out that when I uninstalled the python-pip package with sudo pacman -R python-pip python-reportlab (had to include reportlab to satisfy dependencies) everything started to work as expected. Not sure why, but this is probably due to a double install where the system package is taking precedence.

I had a similar problem after updating to pip==8.0.0. Had to resort to debugging pip to trace out the bad path.

As it turns out my profile directory had a distutils configuration file with some empty path values. This was causing all packages to be installed to the same root directory instead of the appropriate virtual environment (in my case /lib/site-packages).

I'm unsure how the config file got there or how it had empty values but it started after updating pip.

In case anyone else stumbles upon this same problem, simply deleting the file ~/.pydistutils.cfg (or removing the empty config path) fixed the problem in my environment because pip went back to the default distributed configuration.

Here are some practices that could avoid headaches when using Virtual Environments:

• Create a folder for your projects.
• Create your Virtualenv projects inside of this folder.
• After activating the environment of your project, never use "sudo pip install package".
• After finishing your work, always "deactivate" your environment.
• Avoid renaming your project folder.

---

For a better representation of this practices, here is a simulation:

creating a folder for your projects/environments

$ mkdir venv

creating environment

$ cd venv/ 

$ virtualenv google_drive
New python executable in google_drive/bin/python
Installing setuptools, pip...done.

activating environment

$ source google_drive/bin/activate

installing packages

(google_drive) $ pip install PyDrive
Downloading/unpacking PyDrive
Downloading PyDrive-1.3.1-py2-none-any.whl
...
...
...    
Successfully installed PyDrive PyYAML google-api-python-client oauth2client six uritemplate httplib2 pyasn1 rsa pyasn1-modules
Cleaning up...

package available inside the environment

(google_drive) $ python
Python 2.7.6 (default, Oct 26 2016, 20:30:19) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
>>> import pydrive.auth
>>>  
>>> gdrive = pydrive.auth.GoogleAuth()
>>>

deactivate environment

(google_drive) $ deactivate 

$ 

package NOT AVAILABLE outside the environment

(google_drive) $ python
Python 2.7.6 (default, Oct 26 2016, 20:32:10) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
>>> import pydrive.auth
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named pydrive.auth
>>> 

---

Notes:

Why not sudo?

> Virtualenv creates a whole new environment for you, defining $PATH and some other variables and settings. When you use sudo pip install package, you are running Virtualenv as root, escaping the whole environment which was created, and then, installing the package on global site-packages, and not inside the project folder where you have a Virtual Environment, although you have activated the environment.

If you rename the folder of your project (as mentioned in the accepted answer)...

>...you'll have to adjust some variables from some files inside the bin directory of your project. > >For example: > > bin/pip, line 1 (She Bang) > > bin/activate, line 42 (VIRTUAL_ENV)

Came across the same issue today. I simply reinstalled pip globally with sudo easy_install pip (OSX/ Max), then created my virtualenv again with sudo virtualenv nameOfVEnv. Then after activating the new virtualenv the pip command worked as expected.

I don't think I used sudo on the first virtualenv creation and that may have been the reason for not having access to pip from within the virtualenv, I was able to get access to pip2 before this fix though which was odd.

I had this problem. It turned out there was a space in one of my folder names that caused the problem. I removed the space, deleted and reinstantiated using venv, and all was well.

This problem occurs when create a virtualenv instance and then change the parent folder name.

None of the above solutions worked for me.

My venv was active. pip -V and which pip gave me the correct virtualenv path, but when I pip install-ed packages with activated venv, my pip freeze stayed empty.

All the environment variables were correct too.

Finally, I just changed pip and removed virtualenv:

easy_install pip==7.0.2

pip install pip==10

sudo pip uninstall virtualenv

Reinstall venv:

sudo pip install virtualenv

Create venv:

python -m virtualenv venv_name_here

And all packages installed correctly into my venv again.

After creating virtual environment, try to use pip located in yourVirtualEnvName\Scripts

It should install a package inside Lib\site-packages in your virtual environment

I had a similar problem on Windows. It was caused by renaming folder structures in my project within a virtualenv folder name. The paths in files didn't change but stayed as they were when virtual env was created. As Chase Ries mentioned I've changed the paths to VIRTUAL_ENV and python.exe in files

1. ./venv/Scripts/activate.bat, set "VIRTUAL_ENV=path_to_venv\venv" 11 line in file
2. ./venv/Scripts/Activate.ps1, $env:VIRTUAL_ENV="path_to_venv\venv" 30 line in file
3. ./venv/Scripts/pip.exe, #!d:\path_to_env\venv\scripts\python.exe this line is at the end of a file, in my case moved to the right in 667 line, I am working on disc d so at the begining of the path is the letter of it
4. ./venv/Scripts/pip3.7.exe, #!d:\path_to_env\venv\scripts\python.exe this line is at the end of a file, in my case moved to the right in 667 line
5. ./venv/Scripts/pip3.exe, #!d:\path_to_env\venv\scripts\python.exe this line is at the end of a file, in my case moved to the right in 667 line

I had this problem too. Calling sudo pip install caused Python packages to be installed in the global site-packages diretory and calling pip install just worked fine. So no use sudo in virtualenv.

The same problem. Python3.5 and pip 8.0.2 installed from Linux rpm's.

I did not find a primary cause and cannot give a proper answer. It looks like there are multiple possible causes.

However, I hope I can help with sharing my observation and a workaround.

1. pyvenv with --system-site-packages

• ./bin does not contain pip, pip is available from system site packages
• packages are installed globally (BUG?)

2. pyvenv without --system-site-packages

• pip gets installed into ./bin, but it's a different version (from ensurepip)
• packages are installed within the virtual environment (OK)

Obvious workaround for pyvenv with --system-site-packages:

• create it without the --system-site-packages option
• change include-system-site-packages = false to true in pyvenv.cfg file

It's also worth checking that you didn't modify somehow the path to your virtualenv.

In that case the first line in bin/pip (and the rest of the executables) would have an incorrect path.

You can either edit these files and fix the path or remove and install again the virtualenv.

For Python 3ers

Try updating. I had this exact same problem and tried Chases' answer, however no success. The quickest way to refactor this is to update your Python Minor / Patch version if possible. I noticed that I was running 3.5.1 and updated to 3.5.2. Pyvenv once again works.

This happened to me when I created the virtualenv in the wrong location. I then thought I could move the dir to another location without it mattering. It mattered.

mkdir ~/projects
virtualenv myenv
cd myenv
git clone [my repository]

Oh crap, I forgot to cd into projects before creating the virtualenv and cloning the rep. Oh well, I'm too lazy to destroy and recreate. I'll just move the dir with no issues.

cd ~
mv myenv projects
cd projects/myenv/myrepo
pip install -r requirements

Nope, wants more permissions, what the? I thought it was strange but SUDO AWAY! It then installed the packages into a global location.

The lesson I learned was, just delete the virtualenv dir. Don't move it.

Had this issue after installing Divio: it had changed my PATH or environment in some way, as it launches a terminal.

The solution in this case was just to do source ~/.bash_profile which should already be setup to get you back to your original pyenv/pyenv-virtualenv state.

Somehow a setup.cfg file with a prefix="" in the project folder

running pip install on the virtualenv outside the project folder worked so from the inside it was telling pip to use an empty prefix which defaults to "/"

removing the file fixed it

I had this problem, and after trying all the above solution I just removed everything and started afresh.

In my own case i used sudo in creating one of the folders in which the virtual environment existed, and sudo give the priviledges to root

I was very pissed! But it worked!

I have to use 'sudo' for installing packages through pip on my ubuntu system for some reason. This is causing the packages to be installed in global site-packages. Putting this here for anyone who might face this issue in future.

I had exactly the problem from the title, and I solved it. Pip started to install in the venv site-packages after I cleaned my PATH: it had a path to my local ~/bin directory at the very beginning.

So, my advice: thoroughly check your environment variables for "garbage" or any non-standard things. Unfortunately, virtualenv can be sensitive to those.

Good luck!

Lot of good discussion above, but virtualenv examples were used. Since 'conda' is now the recommended tool to manage virtualenv, I have summarized the steps in running pip in conda env as follow.

I'll use py36r as the name of the env, and /opt/conda/envs is the prefix to the envs):

$ source /opt/conda/etc/profile.d/conda.sh # skip if already done 
$ conda activate py36r
$ pip  install pkg_xyz
$ pip  list | grep pkg_xyz

Note that the pip executed should be in /opt/conda/envs/py36r/bin/pip (not /opt/conda/bin/pip).

Alternatively, you can simply run the following without conda activate

$ /opt/conda/envs/py36r/bin/pip

Also, if you install using conda, you can install without activate:

$ conda install -n py36r pkg_abc ...

Short answer is run Command virtualenv with parameter “—no-site-packages”.

Long answer with explanation :-

So after running here and there, and going through lot of threads i found my self the problem. Above answers have given the idea but I would like to go again over everything though.

• The problem is even if you’re activating the environment it’s referring to the system environment because of the way we have crated the virtualenv.

• when we run the command virtualenv env -p python3 it will install the virtualenv but it will not create no-global—site-packages.txt.

• Because of that when you activate the environment by source activate command there this file called site.py (name can be different, i just forgot ) which runs and checks if this file is not present it will not add your env path to sys.path and use systems python.

• to fix this issue just run virtualenv with extra parameter —no-site-packages it will create that file and when you activate the environment it will add your custom environment path in your PATH variable making it accessible.

WINDOWS

For me solution was not to use mkvirtualenv, but:

python -m venv path/to/your/virtualenv

workon works correctly.

while in virtualenv: pip -V shows virtualenv's path to pip

I also encountered this problem, it troubled me for a long time, until I solved it according to @Chase Ries method.

The key to solving the problem is： >Try checking your bin/pip and bin/activate scripts. In bin/pip, look at the shebang. Is it correct? If not, correct it. Then on line ~42 in your bin/activate, check to see if your virtualenv path is right. It'll look something like this > >py >VIRTUAL_ENV="/Users/me/path/to/virtual/environment" > > >If it's wrong, correct it, deactivate, then . bin/activate, and if our mutual problem had the same cause, it should work.

Below, I will explain this process in detail in the Ubuntu environment, the same is true for Windows and MacOS.

The meaning of this sentence is that we need to check whether the first line #!/path/python of the bin/pip file in the virtual environment is correct.

As originally shown in my file:

#!/home/banni/dai/.venv/bin/python3

Run pip in terminal（absolute path）：

/home/banni/dai/.venv/bin/pip

Will find an error：

bash: ./pip: /home/banni/dai/.venv/bin/python3: bad interpreter: No such file or directory

Now I am confused why I can't find this python3, because python3 exists in the folder .venv/bin where the virtual environment is located.

I check the absolute path of the folder .venv/bin. After executing the pwd command, it displays:

/home/banni/Research/dai/.venv/bin

Carefully observe that the path of the .venv folder has changed. Change the first line of the /bin/pip file to

#!/home/banni/Research/dai/.venv/bin/python3

In the same way, check and modify the bin/activate file.

I changed VIRTUAL_ENV="/home/banni/dai/.venv" to VIRTUAL_ENV="/home/banni/Research/dai/.venv"

At this point, after activating the virtual environment, the pip command can be executed normally.

So, for me, the reason for this problem is that the path of the folder where the virtual environment is located has changed (a secret problem that was left when the folders were organized before).

However, due to the change in the location of the folder where the virtual environment is located, there may be many path errors, so the easiest way is to restore the folder where the virtual environment is located to the original location.

1. Activate virtual env

2. Use where pip to find out pip location, if in base env, probably 'pip' is not installed

3. Type

> conda install pip

Enjoy!

I checked all the answers here but none of them worked for me. Especially checked Chase Ries's answer and directories were correct in pip.exe and activate.bat ( for Windows )

I solved the issue by copying the pip.ini ( for Windows, I think it's something else for other OS) which was located in C:\Users\oguno\AppData\Roaming\pip to C:\Users\oguno\Desktop\iec61850\myenv3 where my venv located and change the the target as C:\Users\oguno\Desktop\iec61850\myenv3\Lib\site-packages which shows the site-packages in my virtual environment.

For those who checked the python and pip has correct virtualenv path, another possible problem lies in pip configuration

In my case, i added --prefix in config file to install packages in different paths. This is picked up by virtualenv pip which resulted in installing in the same place as global pip.

It happened to me when I installed virtualenv with --python=python3.6 flag but afterwards tried to use pip2 install.
Creating virtualenv with flag of the version that you'll use solves permission problems. To check, try which pip or which pip2 or which pip3 (depends on your choice). If any pip you use shows path not to venv here is your problem.