I got stuck trying to install various things with Mac El captain pip, so make a note

El capitan's python directory is / usr / bin, so let's go !! (Higanjima)

When I tried to install with pip such as Jupyter and Tensorflow after changing the OS of Mac to El captain, I got many errors that I had never seen.

% pip install https://storage.googleapis.com/tensorflow/mac/tensorflow-0.5.0-py2-none-any.whl                                    
Collecting tensorflow==0.5.0 from https://storage.googleapis.com/tensorflow/mac/tensorflow-0.5.0-py2-none-any.whl
  Using cached https://storage.googleapis.com/tensorflow/mac/tensorflow-0.5.0-py2-none-any.whl
Collecting six>=1.10.0 (from tensorflow==0.5.0)
  Using cached six-1.10.0-py2.py3-none-any.whl
Collecting numpy>=1.9.2 (from tensorflow==0.5.0)
  Using cached numpy-1.10.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Installing collected packages: six, numpy, tensorflow
  Found existing installation: six 1.4.1
    DEPRECATION: Uninstalling a distutils installed project (six) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
    Uninstalling six-1.4.1:
Exception:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/basecommand.py", line 211, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/commands/install.py", line 311, in run
    root=options.root_path,
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_set.py", line 640, in install
    requirement.uninstall(auto_confirm=True)
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_install.py", line 716, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_uninstall.py", line 125, in remove
    renames(path, new_path)
  File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/utils/__init__.py", line 315, in renames
    shutil.move(old, new)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move
    copy2(src, real_dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2
    copystat(src, dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat
    os.chflags(dst, st.st_flags)
OSError: [Errno 1] Operation not permitted: '/var/folders/98/f5yhj5k51r18qfgxm8xx83v40000gn/T/pip-s4Fqnv-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six-1.4.1-py2.7.egg-info'

When I tried which python, the python attached to the OS was directly under / usr / bin /, and this seems to be the cause. After reinstalling python with brew, python fits in / usr / local / bin and all subsequent installations worked.

brew update
brew install python
which python
/usr/local/bin/python

Later talk

After that, when I tried to insert ggplot2 and rjags in R, I got the following error.

Warning message: 
 doTryCatch(return(expr), name, parentenv, handler)so: 
Shared library'/Library/Frameworks/R.framework/Resources/modules//R_X11.so'Cannot be read: 
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
  Reason: image not found 
　　：
　Reason: no suitable image found.  Did find:
	/opt/X11/lib/libSM.6.dylib: stat() failed with errno=62 

http://stackoverflow.com/questions/26489928/cant-load-x11-in-r-after-os-x-yosemite-upgrade

I have done the following with reference to here.

sudo ln -s /usr/X11 /opt/X11 
locate libSM.6.dylib