Brewed pip tries to write to /lib, fails under El Capitan

[pedrovanzella]

I updated to El Capitan and fixed homebrew. I can install formulae just fine. Problem is, pip install anything fails, same as pip3 install anything.

Collecting setuptools
  Downloading setuptools-18.4-py2.py3-none-any.whl (462kB)
    100% |████████████████████████████████| 462kB 43kB/s
Installing collected packages: setuptools
  Found existing installation: setuptools 18.3.1
    Uninstalling setuptools-18.3.1:
      Successfully uninstalled setuptools-18.3.1
  Rolling back uninstall of setuptools
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 211, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 311, in run
    root=options.root_path,
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install
    **kwargs
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 803, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 998, in move_wheel_files
    isolated=self.isolated,
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber
    shutil.copyfile(srcfile, destfile)
  File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/lib/python2.7/site-packages/easy_install.py'

pip3 fails in a similar manner:

Collecting nose
  Downloading nose-1.3.7-py3-none-any.whl (154kB)
    100% |████████████████████████████████| 155kB 2.1MB/s
Installing collected packages: nose
  Found existing installation: nose 1.3.4
    Uninstalling nose-1.3.4:
      Successfully uninstalled nose-1.3.4
  Rolling back uninstall of nose
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/pip/basecommand.py", line 211, in main
    status = self.run(options, args)
  File "/usr/local/lib/python3.5/site-packages/pip/commands/install.py", line 311, in run
    root=options.root_path,
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_set.py", line 646, in install
    **kwargs
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_install.py", line 803, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_install.py", line 998, in move_wheel_files
    isolated=self.isolated,
  File "/usr/local/lib/python3.5/site-packages/pip/wheel.py", line 339, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/local/lib/python3.5/site-packages/pip/wheel.py", line 282, in clobber
    ensure_dir(dest)  # common for the 'include' path
  File "/usr/local/lib/python3.5/site-packages/pip/utils/__init__.py", line 71, in ensure_dir
    os.makedirs(path)
  File "/usr/local/Cellar/python3/3.5.0/Frameworks/Python.framework/Versions/3.5/lib/python3.5/os.py", line 231, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/local/Cellar/python3/3.5.0/Frameworks/Python.framework/Versions/3.5/lib/python3.5/os.py", line 241, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/lib/python3.5'

It seems to be either trying to read from or write to /lib, which is not allowed by SIP, nor does it even exist in El Capitan.

I've tried to re-install python 2 and python 3, and that didn't help.

Trying to install to a virtualenv yields the same result, which is even worse. I see no reason why pip should ever come close to /lib.

[DomT4]

Homebrew certainly wouldn't be supporting it needing to write to a root-necessary directory given half the point of brew is to not force root for every operation under the sun on every Tom, Sally or Michelle.

I haven't seen this anywhere else yet, so perhaps something is awry locally. Can you brew config & brew doctor? Thanks.

[pedrovanzella]

brew config:

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew.git
HEAD: 40e3d975db68d67c9cf394c174ad4207235d2e8d
Last commit: 12 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: 8-core 64-bit sandybridge
OS X: 10.11-x86_64
Xcode: 7.0.1
CLT: N/A
couldn't understand kern.osversion `15.0.0'
GCC-4.2: build 5666
Clang: 7.0 build 700
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p645
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /Users/pedrovanzella/.rbenv/shims/ruby => /Users/pedrovanzella/.rbenv/versions/2.2.3/bin/ruby
Java: 1.8.0_25, 1.8.0_05

brew doctor:

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Python is installed at /Library/Frameworks/Python.framework

Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.

Warning: A .pydistutils.cfg file was found in $HOME, which may cause Python
builds to fail. See:
  https://bugs.python.org/issue6138
  https://bugs.python.org/issue4655

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libCGF.dylib
    /usr/local/lib/libgnuradio-osmosdr.0.1.5git.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
    /usr/local/include/osmosdr/api.h
    /usr/local/include/osmosdr/device.h
    /usr/local/include/osmosdr/pimpl.h
    /usr/local/include/osmosdr/ranges.h
    /usr/local/include/osmosdr/sink.h
    /usr/local/include/osmosdr/source.h
    /usr/local/include/osmosdr/time_spec.h

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .pc files:
    /usr/local/lib/pkgconfig/gnuradio-osmosdr.pc

Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
    gnupg2
    gpg-agent

[pedrovanzella]

Got it fixed!

I had a /Library/Frameworks/Python.framework, which I removed, and a ~/.pydistutils.cfg, which I also removed. That fixed everything.

[DomT4]

Great! Glad things are working again 😃. brew doctor does quite a few Python-related checks so it's worth checking there if you run into things.

[jbnunn]

I didn't have /Library/Frameworks/Python.framework, but removing ~/.pydistutils.cfg fixed for me as well