pip install writes to system path with `-e` #23

forrestbao · 2022-07-09T20:51:40Z

It is really weird that pip detects to switch to user installation (first line printed out below) because I did not sudo. But then the error says that it wants to write to /usr/lib.

I could do python3 -m pip install --user . but not $ python3 -m pip install --user -e . either.

I executed the command below from the root directory a cloned copy of PyDataFront.

$ python3 -m pip install -e .                                                                         
Defaulting to user installation because normal site-packages is not writeable
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Obtaining file:///home/forrest/Textea/PyDataFront
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Installing collected packages: pydatafront
  Attempting uninstall: pydatafront
    Found existing installation: pydatafront 0.0.0
    Uninstalling pydatafront-0.0.0:
      Successfully uninstalled pydatafront-0.0.0
  Running setup.py develop for pydatafront
    error: subprocess-exited-with-error
    
    × python setup.py develop did not run successfully.
    │ exit code: 1
    ╰─> [32 lines of output]
        running develop
        /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        WARNING: The user site-packages directory is disabled.
        /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        error: can't create or remove files in install directory
        
        The following error occurred while trying to add or remove files in the
        installation directory:
        
            [Errno 13] Permission denied: '/usr/local/lib/python3.10/dist-packages/test-easy-install-769272.write-test'
        
        The installation directory you specified (via --install-dir, --prefix, or
        the distutils default setting) was:
        
            /usr/local/lib/python3.10/dist-packages/
        
        Perhaps your account does not have write access to this directory?  If the
        installation directory is a system-owned directory, you may need to sign in
        as the administrator or "root" account.  If you do not have administrative
        access to this machine, you may wish to choose a different installation
        directory, preferably one that is listed in your PYTHONPATH environment
        variable.
        
        For information on other options, you may wish to consult the
        documentation at:
        
          https://setuptools.pypa.io/en/latest/deprecated/easy_install.html
        
        Please make the appropriate changes for your system and try again.
        
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
  WARNING: No metadata found in /home/forrest/.local/lib/python3.10/site-packages
  Rolling back uninstall of pydatafront                                                                                                           
  Moving to /home/forrest/.local/lib/python3.10/site-packages/pydatafront-0.0.0.dist-info/
   from /home/forrest/.local/lib/python3.10/site-packages/~ydatafront-0.0.0.dist-info
error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [32 lines of output]
    running develop
    /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    WARNING: The user site-packages directory is disabled.
    /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    error: can't create or remove files in install directory
    
    The following error occurred while trying to add or remove files in the
    installation directory:
    
        [Errno 13] Permission denied: '/usr/local/lib/python3.10/dist-packages/test-easy-install-769272.write-test'
    
    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:
    
        /usr/local/lib/python3.10/dist-packages/
    
    Perhaps your account does not have write access to this directory?  If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account.  If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.
    
    For information on other options, you may wish to consult the
    documentation at:
    
      https://setuptools.pypa.io/en/latest/deprecated/easy_install.html
    
    Please make the appropriate changes for your system and try again.
    
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

The text was updated successfully, but these errors were encountered:

TURX · 2022-07-09T21:01:29Z

You might have forgotten to activate your venv?

forrestbao · 2022-07-09T21:14:58Z

This should not be related to venv. The first line in the printout shows that pip already knows to install to a user directory rather than a system one.

It seems to be this problem: pypa/pip#7953

TURX · 2022-07-10T06:29:45Z

I have no issue installing and running it with -e on Docker image python:3.10-bullseye.

root@2b83b188f1de:/app# pip uninstall pydatafront
Found existing installation: pydatafront 0.0.1
Uninstalling pydatafront-0.0.1:
  Would remove:
    /root/.local/lib/python3.10/site-packages/pydatafront-0.0.1.dist-info/*
    /root/.local/lib/python3.10/site-packages/pydatafront/*
Proceed (Y/n)? y
  Successfully uninstalled pydatafront-0.0.1
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
root@2b83b188f1de:/app# python3 -m pip install --user -e .
Obtaining file:///app
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: flask in /root/.local/lib/python3.10/site-packages (from pydatafront==0.0.1) (2.1.2)
Requirement already satisfied: flask-cors in /root/.local/lib/python3.10/site-packages (from pydatafront==0.0.1) (3.0.10)
Requirement already satisfied: Jinja2>=3.0 in /root/.local/lib/python3.10/site-packages (from flask->pydatafront==0.0.1) (3.1.2)
Requirement already satisfied: itsdangerous>=2.0 in /root/.local/lib/python3.10/site-packages (from flask->pydatafront==0.0.1) (2.1.2)
Requirement already satisfied: Werkzeug>=2.0 in /root/.local/lib/python3.10/site-packages (from flask->pydatafront==0.0.1) (2.1.2)
Requirement already satisfied: click>=8.0 in /root/.local/lib/python3.10/site-packages (from flask->pydatafront==0.0.1) (8.1.3)
Requirement already satisfied: Six in /root/.local/lib/python3.10/site-packages (from flask-cors->pydatafront==0.0.1) (1.16.0)
Requirement already satisfied: MarkupSafe>=2.0 in /root/.local/lib/python3.10/site-packages (from Jinja2>=3.0->flask->pydatafront==0.0.1) (2.1.1)
Installing collected packages: pydatafront
  Running setup.py develop for pydatafront
Successfully installed pydatafront-0.0.1
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
WARNING: You are using pip version 22.0.4; however, version 22.1.2 is available.
You should consider upgrading via the '/usr/local/bin/python3 -m pip install --upgrade pip' command.
root@2b83b188f1de:/app# python3 -m pydatafront
usage: __main__.py [-h] [--host HOST] [--port PORT] this_class main_class
__main__.py: error: the following arguments are required: main_class

forrestbao · 2022-07-10T06:36:04Z

This is because you are root.

TURX · 2022-07-10T06:37:30Z

I have it installed in ~/.local.

root@2b83b188f1de:~/.local/lib/python3.10/site-packages# ls | grep pydatafront
pydatafront.egg-link

forrestbao · 2022-07-10T06:38:56Z

Still, your ~ is /root/

TURX · 2022-07-10T06:40:58Z

Let me test in my school lab.

TURX · 2022-07-10T06:51:09Z

I have installed the current main branch on my home dir in my school lab where I have no privileged access.

[ruixuan@rockhopper-01] (32)$ python3 -m pip install --user -e .
Obtaining file:///afs/cs.wisc.edu/u/r/u/ruixuan/test/PyDataFront
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: flask in /usr/lib/python3/dist-packages (from pydatafront==0.0.1) (1.1.1)
Collecting flask-cors
  Downloading Flask_Cors-3.0.10-py2.py3-none-any.whl (14 kB)
Requirement already satisfied: Six in /usr/lib/python3/dist-packages (from flask-cors->pydatafront==0.0.1) (1.14.0)
Installing collected packages: flask-cors, pydatafront
  Running setup.py develop for pydatafront
Successfully installed flask-cors-3.0.10 pydatafront
[ruixuan@rockhopper-01] (33)$ ls
backend/  examples/  frontend/  main.py  pyproject.toml  README.md  setup.cfg
[ruixuan@rockhopper-01] (34)$ python3 -m pydatafront
usage: __main__.py [-h] [--host HOST] [--port PORT] this_class main_class
__main__.py: error: the following arguments are required: main_class
[ruixuan@rockhopper-01] (35)$ python3 -m pip uninstall pydatafront
Found existing installation: pydatafront 0.0.1
Uninstalling pydatafront-0.0.1:
  Would remove:
    /afs/cs.wisc.edu/u/r/u/ruixuan/.local/lib/python3.8/site-packages/pydatafront.egg-link
Proceed (Y/n)? y
  Successfully uninstalled pydatafront-0.0.1

TURX · 2022-07-10T06:51:34Z

You might try upgrading your pip first? python3 -m pip install --upgrade pip

forrestbao · 2022-07-10T19:36:59Z

I tried to upgrade. No clue. I can setPYTHONPATH for now as a temporarily workaround.

forrestbao · 2022-08-05T16:29:33Z

I just tried on a freshly install Lubuntu 22.04 box. Same problem. Pip is already upgraded.

$ python3 -m pip install --upgrade pip
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pip in /usr/lib/python3/dist-packages (22.0.2)
Collecting pip
  Downloading pip-22.2.2-py3-none-any.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 3.3 MB/s eta 0:00:00
Installing collected packages: pip
  WARNING: The scripts pip, pip3 and pip3.10 are installed in '/home/forrest/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.  
Successfully installed pip-22.2.2

It's really weird that pip insists to write to /usr/local/lib/python3.10/dist-packages/ instead of my home directory.

$ python3 -m pip install  --user -e .
Obtaining file:///home/forrest/repos/PyDataFront
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Installing collected packages: pydatafront
  Running setup.py develop for pydatafront
    error: subprocess-exited-with-error
    
    × python setup.py develop did not run successfully.
    │ exit code: 1
    ╰─> [32 lines of output]
        running develop
        /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        WARNING: The user site-packages directory is disabled.
        /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        error: can't create or remove files in install directory
        
        The following error occurred while trying to add or remove files in the
        installation directory:
        
            [Errno 13] Permission denied: '/usr/local/lib/python3.10/dist-packages/test-easy-install-5961.write-test'
        
        The installation directory you specified (via --install-dir, --prefix, or
        the distutils default setting) was:
        
            /usr/local/lib/python3.10/dist-packages/
        
        Perhaps your account does not have write access to this directory?  If the
        installation directory is a system-owned directory, you may need to sign in
        as the administrator or "root" account.  If you do not have administrative
        access to this machine, you may wish to choose a different installation
        directory, preferably one that is listed in your PYTHONPATH environment
        variable.
        
        For information on other options, you may wish to consult the
        documentation at:
        
          https://setuptools.pypa.io/en/latest/deprecated/easy_install.html
        
        Please make the appropriate changes for your system and try again.
        
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [32 lines of output]
    running develop
    /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    WARNING: The user site-packages directory is disabled.
    /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    error: can't create or remove files in install directory
    
    The following error occurred while trying to add or remove files in the
    installation directory:
    
        [Errno 13] Permission denied: '/usr/local/lib/python3.10/dist-packages/test-easy-install-5961.write-test'
    
    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:
    
        /usr/local/lib/python3.10/dist-packages/
    
    Perhaps your account does not have write access to this directory?  If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account.  If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.
    
    For information on other options, you may wish to consult the
    documentation at:
    
      https://setuptools.pypa.io/en/latest/deprecated/easy_install.html
    
    Please make the appropriate changes for your system and try again.
    
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

forrestbao · 2023-03-05T07:28:38Z

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pip install writes to system path with `-e` #23

pip install writes to system path with `-e` #23

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pip install writes to system path with -e #23

pip install writes to system path with -e #23

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pip install writes to system path with `-e` #23

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