pip missed after upgrading both python2 and python3 #5419

ghost · 2016-09-30T11:47:54Z

Please follow the general troubleshooting steps first:

Ran brew update and retried your prior step?
Ran brew doctor, fixed as many issues as possible and retried your prior step?
If you're seeing permission errors tried running sudo chown -R $(whoami) $(brew --prefix)?

Bug reports:

pip lost after upgrading python.
pip3 lost after upgrading python3.
Although brew notices me to run brew postinstall python & brew postinstall python3, these commands failed to execute.

> sudo chown -R $(whoami) $(brew --prefix)
> brew postinstall python
==> Using the sandbox
Error: Operation not permitted - (../../../../../../../../../../lib/python2.7/site-packages, /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages)
> brew postinstall python3
==> Using the sandbox
Error: Operation not permitted - (../../../../../../../../../../lib/python3.5/site-packages, /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages)

brew gist-logs python result here

brew gist-logs python3 result here

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

ghost · 2016-10-01T11:57:00Z

> brew postinstall python3 -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161001-36280-ag6wb6.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/postinstall.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb -v
==> Sandbox log
Oct  1 19:55:54 kernel[0]: Sandbox: ruby(36281) deny(1) file-write-create /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
Error: Operation not permitted - (../../../../../../../../../../lib/python3.5/site-packages, /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages)
> ll /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
ls: /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages: No such file or directory
>
> mkdir /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
> ll /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5 | grep site-packages
drwxr-xr-x    2 haodong  admin    68B Oct  1 19:57 site-packages
> brew postinstall python3 -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161001-36466-167ihk0.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/postinstall.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb -v
==> Sandbox log
Oct  1 19:58:02 kernel[0]: Sandbox: ruby(36467) deny(1) file-write-unlink /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
Oct  1 19:58:02 kernel[0]: Sandbox: ruby(36467) deny(1) file-write-unlink /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
Error: Operation not permitted - /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages

ghost · 2016-10-01T12:06:55Z

i just tried #1415 (comment) but useless.

> ll /usr/local/lib | grep python
drwxr-xr-x   3 haodong  admin   102B Aug 20 18:16 python2.7
drwxr-xr-x   4 haodong  admin   136B Oct  1 19:54 python3.5
> rm -rf /usr/local/lib/python*
> brew update
> brew install python
...
Warning: The post-install step did not complete successfully
You can try again using `brew postinstall python`
...
> brew postinstall python -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161001-52694-mibrur.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/postinstall.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python.rb -v
==> Sandbox log
Oct  1 20:04:54 kernel[0]: Sandbox: ruby(52695) deny(1) file-write-create /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Error: Operation not permitted - (../../../../../../../../../../lib/python2.7/site-packages, /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages)
>
> mkdir /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
> ll /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7 | grep site-packages
drwxr-xr-x     2 haodong  admin    68B Oct  1 20:05 site-packages
> brew postinstall python -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161001-52852-1obg6pn.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/postinstall.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python.rb -v
==> Sandbox log
Oct  1 20:06:09 kernel[0]: Sandbox: ruby(52853) deny(1) file-write-unlink /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Oct  1 20:06:09 kernel[0]: Sandbox: ruby(52853) deny(1) file-write-unlink /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Error: Operation not permitted - /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages

KDGNOR · 2016-10-01T13:45:35Z

$ pip search test
i get this then i try update not sure if pip fail or homebrew break it... ? 👎

Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 209, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/search.py", line 43, in run
    pypi_hits = self.search(query, options)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/search.py", line 60, in search
    hits = pypi.search({'name': query, 'summary': query}, 'or')
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py", line 1240, in __call__
    return self.__send(self.__name, args)
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py", line 1599, in __request
    verbose=self.__verbose
  File "/usr/local/lib/python2.7/site-packages/pip/download.py", line 764, in request
    headers=headers, stream=True)
  File "/usr/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 511, in post
    return self.request('POST', url, data=data, json=json, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/pip/download.py", line 378, in request
    return super(PipSession, self).request(method, url, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 468, in request
    resp = self.send(prep, **send_kwargs)
  File "/usr/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 576, in send
    r = adapter.send(request, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/pip/_vendor/cachecontrol/adapter.py", line 46, in send
    resp = super(CacheControlAdapter, self).send(request, **kw)
  File "/usr/local/lib/python2.7/site-packages/pip/_vendor/requests/adapters.py", line 447, in send
    raise SSLError(e, request=request)
SSLError: EOF occurred in violation of protocol (_ssl.c:590)

ghost · 2016-10-01T13:51:53Z

@KDGNOR

> pip search test
zsh: command not found: pip

KDGNOR · 2016-10-01T14:23:53Z

mabye i install pip from https://pip.pypa.io not homebrew then?

i install openssl and alot of brew broke....
so i think mabye it broke pip download/search too?

pheki · 2016-10-04T19:56:17Z

Same happened to me (in python3), but I first tried brew reinstall python3 and it gave me this error/warning:

error: could not delete '/usr/local/lib/python3.5/site-packages/pkg_resources/__init__.py': Permission denied
Warning: The post-install step did not complete successfully
You can try again using `brew postinstall python3`

brew doctor gave me nothing (related) but running sudo chown -R $(whoami) $(brew --prefix) and then brew postinstall python3 solved it.

ghost · 2016-10-05T03:31:55Z

@Bilkow

You're lucky. I got:

> sudo chown -R $(whoami) $(brew --prefix)
Password:
> brew postinstall python3
==> Using the sandbox
Error: Operation not permitted - (../../../../../../../../../../lib/python3.5/site-packages, /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages)
> brew postinstall python3 -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161005-1386-eadq47.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/postinstall.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb -v
==> Sandbox log
Oct  5 11:32:10 sandboxd[401]: ruby(1387) deny file-write-create /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages
Error: Operation not permitted - (../../../../../../../../../../lib/python3.5/site-packages, /usr/local/Homebrew/Cellar/python3/3.5.2_2/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages)

shawnzhu · 2016-10-06T00:45:19Z

I have the same issue as #5419 (comment) when running brew postinstall python:

$ brew postinstall python -v
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20161005-5149-10brfim.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/homebrew/Library/Homebrew -- /usr/local/homebrew/Library/Homebrew/postinstall.rb /usr/local/homebrew/Library/Taps/homebrew/homebrew-core/Formula/python.rb -v
Error: Operation not permitted - (../../../../../../../../../../lib/python2.7/site-packages, /usr/local/homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages)

However, I've fixed that by running python -m ensurepip then both pip and setuptools are installed successfully at /usr/local/homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages and you can find commands pip and easy_install from /usr/local/homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/bin although it doesn't create any symbolic links under /usr/local/bin automatically. so I have to manually create those symbolic links:

$ cd /usr/local/homebrew/Cellar/python/2.7.12_1/bin/
$ ln -s ../Frameworks/Python.framework/Versions/2.7/bin/pip
$ ln -s ../Frameworks/Python.framework/Versions/2.7/bin/easy_install
$ cd /usr/local/bin
$ ln -s ../homebrew/Cellar/python/2.7.12_1/bin/pip
$ ln -s ../homebrew/Cellar/python/2.7.12_1/bin/easy_install

michaelbrundage · 2016-10-08T04:42:09Z

I ran in to the same issue with the same symptoms, and bilkow's fix worked for me. Mac OS 10.11.

merrywhether · 2016-10-09T18:24:57Z

+1 on bilkow's solution

tdsmith · 2016-10-11T03:28:12Z

I believe this is related to Homebrew/brew#1101; sandbox log has:

Sep 30 19:39:56 kernel[0]: Sandbox: ruby(32623) deny(1) file-write-create /usr/local/Homebrew/Cellar/python/2.7.12_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages

cc @MikeMcQuaid

MikeMcQuaid · 2016-10-11T08:40:15Z

@tdsmith I've opened Homebrew/brew#1261 and Homebrew/brew#1262 to address this.

Relatedly, everyone in this thread seems to have a /usr/local/[Hh]omebrew/Cellar directory and a /usr/local/prefix. This will result in you not being able to use a bunch of our binary packages. I recommend moving your Cellar to /usr/local/Cellar and, if needed (it may be, I'm not sure) reinstall your packages (do this easily with brew bundle dump; brew uninstall --force $(brew list); brew bundle).

pheki · 2016-10-12T02:08:41Z

@MikeMcQuaid /usr/local/Homebrew/Cellar doesn't exist for me though. My Cellar is /usr/local/Cellar, my prefix /usr/local and my repository /usr/local/Homebrew.

I guess this explains why some have not managed to fix it, but not why/how pip[3] has gone missing.

ghost · 2016-10-12T04:07:30Z

@Bilkow I have.
If you reinstall Homebrew with the new installer script. It will have either.
OK. Now I'm regretting that should not reinstall the new one.

ogail · 2016-11-27T11:11:36Z

I had same problem that pip3 is not recognized after brew update and brew upgrade. This #5419 (comment) has solution

spencerzhang91 · 2016-12-26T12:43:47Z

$ which pip2
/usr/local/bin/pip2
$ which pip3
/usr/local/bin/pip3
$ which pip
/usr/local/bin/pip
$ pip
-bash: /usr/local/bin/pip: /usr/local/opt/python3/bin/python3.5: bad interpreter: No such file or directory
If I pip2 or pip3 no error message would pop up, but just all packages install under python3 has gone.
It's a shamed that I step into this hole after almost a month... should have check issues more often:(
Just a guess: it seems that there's some problem with the shortcut?

ghost · 2016-12-26T12:45:21Z

For myself:
Reinstalled macOS and everything becomes OK. (reinstalling homebrew was not a solution to me)

spencerzhang91 · 2016-12-26T12:59:28Z

We can't really consider reinstall the whole system as a solution, I think...
Have you tried uninstall both versions of python and start clean?

ghost · 2016-12-26T13:01:30Z

Yes, and not helpful. It's frustrating.

spencerzhang91 · 2016-12-26T13:11:58Z

As far as I can remember, the default pip is pip2(pip of python2), right?
I kind of 'fixed' it by $sudo pip2 install --upgrade pip.
After that, except python3 packages are still gone, $pip won't pop up any error message.

spencerzhang91 · 2016-12-26T13:13:36Z

However one thing still bothers me is whether the installed packages are still existing somewhere or just been removed with the upgrade?
Sigh...

ahmedelgabri · 2017-08-02T20:05:23Z

I have the same problem & none of these solutions solved my issue, any clue how to fix it, reinstalling the OS is not an option.

ilovezfs · 2017-08-02T20:51:06Z

@ahmedelgabri please open a new issue and complete the issue template if you're having a problem.

tdsmith added bug Reproducible Homebrew/homebrew-core bug python Python use is a significant feature of the PR or issue sandbox Homebrew's use of the macOS Sandbox labels Oct 11, 2016

ghost closed this as completed Dec 26, 2016

Homebrew locked and limited conversation to collaborators Aug 2, 2017

This issue was closed.

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pip missed after upgrading both python2 and python3 #5419

pip missed after upgrading both python2 and python3 #5419

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ahmedelgabri commented Aug 2, 2017

ilovezfs commented Aug 2, 2017

pip missed after upgrading both python2 and python3 #5419

pip missed after upgrading both python2 and python3 #5419

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ghost commented Sep 30, 2016 • edited by ghost Loading

Please follow the general troubleshooting steps first:

Bug reports:

ghost commented Oct 1, 2016 • edited by ghost Loading

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