RuntimeError: The current Numpy installation fails to pass a sanity check due to a bug in the windows runtime

Question

I am using Python 3.9 on Windows 10 version 2004 x64. PowerShell as Administrator.

Python verion:

Python 3.9.0 (tags/v3.9.0:9cf6752, Oct  5 2020, 15:34:40) [MSC v.1927 64 bit (AMD64)] on win32

Install matplotlib error.

pip install virtualenv
virtualenv foo
cd .\foo
.\Scripts\active
pip install numpy
pip install matplotlib

Error

Windows PowerShell
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PS C:\WINDOWS\system32> Set-ExecutionPolicy Unrestricted -Force
PS C:\WINDOWS\system32> cd /d C:\Windows\System32\cmd.exe
Set-Location : A positional parameter cannot be found that accepts argument 'C:\Windows\System32\cmd.exe'.
At line:1 char:1
+ cd /d C:\Windows\System32\cmd.exe
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : InvalidArgument: (:) [Set-Location], ParameterBindingException
    + FullyQualifiedErrorId : PositionalParameterNotFound,Microsoft.PowerShell.Commands.SetLocationCommand

PS C:\WINDOWS\system32> cd C:\Windows\System32\cmd.exe
cd : Cannot find path 'C:\Windows\System32\cmd.exe' because it does not exist.
At line:1 char:1
+ cd C:\Windows\System32\cmd.exe
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : ObjectNotFound: (C:\Windows\System32\cmd.exe:String) [Set-Location], ItemNotFoundExcepti
   on
    + FullyQualifiedErrorId : PathNotFound,Microsoft.PowerShell.Commands.SetLocationCommand

PS C:\WINDOWS\system32> cd D:\
PS D:\> cd .\Users\donhuvy\
PS D:\Users\donhuvy> ls


    Directory: D:\Users\donhuvy


Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
d-----        10/26/2020   3:35 PM                AppData
d-----         11/7/2020   9:33 AM                PycharmProjects


PS D:\Users\donhuvy> cd .\PycharmProjects\pythonProject\
PS D:\Users\donhuvy\PycharmProjects\pythonProject> virtualenv foo
virtualenv : The term 'virtualenv' is not recognized as the name of a cmdlet, function, script file, or operable
program. Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:1
+ virtualenv foo
+ ~~~~~~~~~~
    + CategoryInfo          : ObjectNotFound: (virtualenv:String) [], CommandNotFoundException
    + FullyQualifiedErrorId : CommandNotFoundException

PS D:\Users\donhuvy\PycharmProjects\pythonProject> pip install virtualenv
Collecting virtualenv
  Downloading virtualenv-20.1.0-py2.py3-none-any.whl (4.9 MB)
     |████████████████████████████████| 4.9 MB 1.1 MB/s
Collecting distlib<1,>=0.3.1
  Downloading distlib-0.3.1-py2.py3-none-any.whl (335 kB)
     |████████████████████████████████| 335 kB 6.4 MB/s
Requirement already satisfied: six<2,>=1.9.0 in c:\users\donhuvy\appdata\roaming\python\python39\site-packages (from virtualenv) (1.15.0)
Collecting filelock<4,>=3.0.0
  Downloading filelock-3.0.12-py3-none-any.whl (7.6 kB)
Collecting appdirs<2,>=1.4.3
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Installing collected packages: distlib, filelock, appdirs, virtualenv
Successfully installed appdirs-1.4.4 distlib-0.3.1 filelock-3.0.12 virtualenv-20.1.0
PS D:\Users\donhuvy\PycharmProjects\pythonProject> virtualenv foo
created virtual environment CPython3.9.0.final.0-64 in 1312ms
  creator CPython3Windows(dest=D:\Users\donhuvy\PycharmProjects\pythonProject\foo, clear=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=C:\Users\donhuvy\AppData\Local\pypa\virtualenv)
    added seed packages: pip==20.2.4, setuptools==50.3.2, wheel==0.35.1
  activators BashActivator,BatchActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
PS D:\Users\donhuvy\PycharmProjects\pythonProject> cd .\foo
PS D:\Users\donhuvy\PycharmProjects\pythonProject\foo> .\Scripts\activate
(foo) PS D:\Users\donhuvy\PycharmProjects\pythonProject\foo> pip install numpy
Collecting numpy
  Using cached numpy-1.19.4-cp39-cp39-win_amd64.whl (13.0 MB)
Installing collected packages: numpy
Successfully installed numpy-1.19.4
(foo) PS D:\Users\donhuvy\PycharmProjects\pythonProject\foo> pip install matplotlib
Collecting matplotlib
  Using cached matplotlib-3.3.2.tar.gz (37.9 MB)
 ** On entry to DGEBAL parameter number  3 had an illegal value
 ** On entry to DGEHRD  parameter number  2 had an illegal value
 ** On entry to DORGHR DORGQR parameter number  2 had an illegal value
 ** On entry to DHSEQR parameter number  4 had an illegal value
    ERROR: Command errored out with exit status 1:
     command: 'D:\Users\donhuvy\PycharmProjects\pythonProject\foo\Scripts\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\donhuvy\\AppData\\Local\\Temp\\pip-install-8bn40qg7\\matplotlib\\setup.py'"'"'; __file__='"'"'C:\\Users\\donhuvy\\AppData\\Local\\Temp\\pip-install-8bn40qg7\\matplotlib\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe'
         cwd: C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\
    Complete output (61 lines):

    Edit setup.cfg to change the build options; suppress output with --quiet.

    BUILDING MATPLOTLIB
      matplotlib: yes [3.3.2]
          python: yes [3.9.0 (tags/v3.9.0:9cf6752, Oct  5 2020, 15:34:40) [MSC
                      v.1927 64 bit (AMD64)]]
        platform: yes [win32]
     sample_data: yes [installing]
           tests: no  [skipping due to configuration]
          macosx: no  [Mac OS-X only]

    running egg_info
    creating C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info
    writing C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\PKG-INFO
    writing dependency_links to C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\dependency_links.txt
    writing namespace_packages to C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\namespace_packages.txt
    writing requirements to C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\requires.txt
    writing top-level names to C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\top_level.txt
    writing manifest file 'C:\Users\donhuvy\AppData\Local\Temp\pip-pip-egg-info-39nmc0pe\matplotlib.egg-info\SOURCES.txt'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\setup.py", line 242, in <module>
        setup(  # Finally, pass this all along to distutils to do the heavy lifting.
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\setuptools\__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\core.py", line 148, in setup
        dist.run_commands()
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\dist.py", line 985, in run_command
        cmd_obj.run()
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\setuptools\command\egg_info.py", line 298, in run
        self.find_sources()
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\setuptools\command\egg_info.py", line 305, in find_sources
        mm.run()
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\setuptools\command\egg_info.py", line 536, in run
        self.add_defaults()
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\setuptools\command\egg_info.py", line 572, in add_defaults
        sdist.add_defaults(self)
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\command\sdist.py", line 228, in add_defaults
        self._add_defaults_ext()
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\command\sdist.py", line 311, in _add_defaults_ext
        build_ext = self.get_finalized_command('build_ext')
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\cmd.py", line 299, in get_finalized_command
        cmd_obj.ensure_finalized()
      File "d:\users\donhuvy\appdata\local\programs\python\python39\lib\distutils\cmd.py", line 107, in ensure_finalized
        self.finalize_options()
      File "C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\setup.py", line 88, in finalize_options
        self.distribution.ext_modules[:] = [
      File "C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\setup.py", line 91, in <listcomp>
        for ext in package.get_extensions()
      File "C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\setupext.py", line 345, in get_extensions
        add_numpy_flags(ext)
      File "C:\Users\donhuvy\AppData\Local\Temp\pip-install-8bn40qg7\matplotlib\setupext.py", line 469, in add_numpy_flags
        import numpy as np
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\numpy\__init__.py", line 305, in <module>
        _win_os_check()
      File "D:\Users\donhuvy\PycharmProjects\pythonProject\foo\lib\site-packages\numpy\__init__.py", line 302, in _win_os_check
        raise RuntimeError(msg.format(__file__)) from None
    RuntimeError: The current Numpy installation ('D:\\Users\\donhuvy\\PycharmProjects\\pythonProject\\foo\\lib\\site-packages\\numpy\\__init__.py') fails to pass a sanity check due to a bug in the windows runtime. See this issue for more information: https://tinyurl.com/ y3dm3h86
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
(foo) PS D:\Users\donhuvy\PycharmProjects\pythonProject\foo>

Error information link to https://developercommunity.visualstudio.com/content/problem/1207405/fmod-after-an-update-to-windows-2004-is-causing-a.html

Use Pycharm 2020.2 Ultimate also catch error.

How to fix it?

Solution

The temporary solution is to use numpy 1.19.3.

pip install numpy==1.19.3

From this Microsoft thread fix will be available around January 2021.

Update: it is fixed in KB4598291 update

Comments

[Jean-Claude Arbaut]

The problem is solved as of numpy 1.19.5, published on 2021-01-05.

[James Grey]

You can post new answer, this issue received much interest.

[Jean-Claude Arbaut]

Actually, I can't (question closed). But it's doesn't matter much.

[James Grey]

The second temporary solution maybe is use Miniconda for Windows.

[hekimgil]

Mine was a similar problem, with MoviePy (1.0.3) installation on a Windows machine and this Numpy version downgrade solved the problem for that too. Thanks...

[nooshinha]

solved my problem on Pycharm and windows. I changed the installed version from 1.19.4 to 1.19.3

[Uri]

This is now April. Has this issue resolved? Can I install numpy 1.20??

[Equinox]

@Uri yes this was resolved in February