OSX El Capitan sudo pip install OSError Errno 1 Operation not permitted

Question

When I run   sudo pip install ipython   I get the following error     OSError   Errno  1  Operation not permitted    System Library Frameworks Python framework Versions 2 7 share    The last command executed tries to create the directory given above   Also  the following command fails to install iPython without providing any errors   sudo pip install --user python    I am on Mac OS X El Capitan in case other folks on this OS see the same issue

User · Answer

I guess you have some conflict with other package. For me it was six. So you need to use a command like this:

pip install google-api-python-client --upgrade --ignore-installed six

or

pip install --ignore-installed six

User · Answer

TL DR  PATH fix   Use pip install --user package name to install a package that should include CLI executables  Launch a python shell and import package name Find where lib python     occurs in the output and replace it all with bin It s likely to be  HOME Library Python 2 7 bin   Details  Because of the new System Integrity Protection in macOS 10 11 El Capitan  you can no longer sudo pip install  We won t debate the merits of that here   Another answer explains that you should pip install --user which is correct  But they sent you to the back alleys to figure out what to do about your  PATH so that you could get access to installed executables  Luckily  I ve already solved a similar need for an unrelated question   Here is a transcript of how I solved the problem on one of my systems  I m including it all rather just than the  PATH that worked for me  because your system may be different from mine  This process should work for everybody     pip install --user jp Collecting jp   Downloading jp-0 2 4 tar gz Installing collected packages  jp   Running setup py install for jp     done Successfully installed jp-0 2 4    python -c  import jp  print jp   lt module  jp  from   Users bbronosky Library Python 2 7 lib python site-packages jp   init   pyc  gt     find  Users bbronosky Library Python -type f -perm -100  Users bbronosky Library Python 2 7 bin jp    which jp    echo -e   n  export PATH  HOME Library Python 2 7 bin  PATH   gt  gt     bashrc    bash   starting a new bash process for demo  but you should open a new terminal    which jp  Users bbronosky Library Python 2 7 bin jp    jp usage  jp  lt expression gt   lt filepath gt

User · Answer

Same error  Installing collected packages  six  pyparsing  packaging  appdirs  setuptools Exception  Traceback  most recent call last     File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip basecommand py   line 215  in main     status   self run options  args    File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip commands install py   line 342  in run     prefix options prefix path    File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip req req set py   line 784  in install       kwargs   File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip req req install py   line 851  in install     self move wheel files self source dir  root root  prefix prefix    File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip req req install py   line 1064  in move wheel files     isolated self isolated    File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip wheel py   line 345  in move wheel files     clobber source  lib dir  True    File   Library Python 2 7 site-packages pip-9 0 1-py2 7 egg pip wheel py   line 323  in clobber     shutil copyfile srcfile  destfile    File   System Library 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    Library Python 2 7 site-packages six py    and here I use --user without sudo to solve this issue    pip install --user scikit-image h5py keras pygame Collecting scikit-image   Downloading http   mirrors aliyun com pypi packages 65 69 27a1d55ce8f77c8ac757938707105b1070ff4f2ae47d2dc99461bfae4491 scikit image-0 13 0-cp27-cp27m-macosx 10 6 intel macosx 10 9 intel macosx 10 9 x86 64 macosx 10 10 intel macosx 10 10 x86 64 whl  28 1MB      100                                                                     28 1MB 380kB s Collecting h5py   Downloading http   mirrors aliyun com pypi packages b7 cc 1c29b0815b12de2c92b5323cad60f724ac8f0e39d0166d0b9dfacbcb70dd h5py-2 7 0-cp27-cp27m-macosx 10 6 intel macosx 10 9 intel macosx 10 9 x86 64 macosx 10 10 intel macosx 10 10 x86 64 whl  4 5MB      100                                                                     4 5MB 503kB s Requirement already satisfied  keras in  Library Python 2 7 site-packages Requirement already satisfied  pygame in  Library Python 2 7 site-packages Requirement already satisfied  matplotlib gt  1 3 1 in  System Library Frameworks Python framework Versions 2 7 Extras lib python  from scikit-image  Requirement already satisfied  six gt  1 7 3 in  Library Python 2 7 site-packages  from scikit-image  Requirement already satisfied  pillow gt  2 1 0 in  Library Python 2 7 site-packages  from scikit-image  Requirement already satisfied  networkx gt  1 8 in  Library Python 2 7 site-packages  from scikit-image  Requirement already satisfied  PyWavelets gt  0 4 0 in  Library Python 2 7 site-packages  from scikit-image  Collecting scipy gt  0 17 0  from scikit-image    Downloading http   mirrors aliyun com pypi packages 72 eb d398b9f63ee936575edc62520477d6c2353ed013bacd656bd0c8bc1d0fa7 scipy-0 19 0-cp27-cp27m-macosx 10 6 intel macosx 10 9 intel macosx 10 9 x86 64 macosx 10 10 intel macosx 10 10 x86 64 whl  16 2MB      100                                                                     16 2MB 990kB s Requirement already satisfied  numpy gt  1 7 in  Library Python 2 7 site-packages  from h5py  Requirement already satisfied  theano in  Library Python 2 7 site-packages  from keras  Requirement already satisfied  pyyaml in  Library Python 2 7 site-packages  from keras  Requirement already satisfied  python-dateutil in  System Library Frameworks Python framework Versions 2 7 Extras lib python  from matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  tornado in  Library Python 2 7 site-packages  from matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  pyparsing gt  1 5 6 in  Users qiuwei Library Python 2 7 lib python site-packages  from matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  nose in  Library Python 2 7 site-packages  from matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  olefile in  Library Python 2 7 site-packages  from pillow gt  2 1 0- gt scikit-image  Requirement already satisfied  decorator gt  3 4 0 in  Library Python 2 7 site-packages  from networkx gt  1 8- gt scikit-image  Requirement already satisfied  singledispatch in  Library Python 2 7 site-packages  from tornado- gt matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  certifi in  Library Python 2 7 site-packages  from tornado- gt matplotlib gt  1 3 1- gt scikit-image  Requirement already satisfied  backports abc gt  0 4 in  Library Python 2 7 site-packages  from tornado- gt matplotlib gt  1 3 1- gt scikit-image  Installing collected packages  scipy  scikit-image  h5py Successfully installed h5py-2 7 0 scikit-image-0 13 0 scipy-0 19 0    Hope it will help someone who encounter similar issue

User · Answer

pip install --ignore-installed six  This will do the job  then you can try your first command   Via http   github com pypa pip issues 3165

User · Answer

You should reinstall Python   brew reinstall python   To get brew see the brew homepage

User · Answer

I had the same problems  but using easy install  module  solved the problem for me   I am not sure why  but pip and easy install use different install locations  and easy install chose the right ones   Edit  without re-checking but because of the comments  it seems that different  OSX and brew-installed  installations interfere with each other which is why they tools mentioned indeed point to different locations  since they belong to different installations   I understand that usually those tools from one install point to the same folder

User · Answer

Instructions telling sudo pip install are inherently wrong   If there is any tutorial out there which says you should do sudo pip then please file a bug against this package  The author is dis-educating Python community  as time has proven sudo pip to be a broken practice   OSX El Capitan introduced a mechanisms to prevent damaging the operating system files   System Library Frameworks Python framework Versions 2 7 share is one of the protected locations  A normal user has no reason to put or write any files there  This is because the operating system itself relies on these files and sudo pip  with all force given from the above  would unconditionally overwrite them  Usually bad things would not happen  but the chances are there  Apple wants to protect their OS users to accidentally bricking their installation   Instead  you need to install a Python package  like IPython  locally to the home folder of your user  The easiest way is to create a virtual environment  activate it and then run pip in the virtual environment    Example   cd      Go to home directory virtualenv my-venv source my-venv bin activate pip install IPython   More info   Official Python package installation tutorial  How to create virtual environments    Alternatively  one should be able to do pip install --user  But again  no sudo needed and you need to manually set up PATH environment variable

User · Answer

I have python2 7 installed via brew and the following solved my problem  brew install numpy  It installs python3  but it still works and sets it up for 2 7 as well

User · Answer

Used pip3 install  lt package gt  instead and solved the permission problem with pip

User · Answer

It is hard to get pip working on El Capitan for several reasons     OS X doesn t set some distutils variables correctly  so pip tries to install ancillary files in locations under  System Library   El Capitan blocks this  which is the error you are running into      OS X includes a number of outdated packages under  System Library   pip often wants to upgrade these but cannot on El Capitan       OS X places  System Library  higher in the python search order than  Library Python 2 7 site-packages  the system-wide python package location   so even if you manage to install newer versions of some packages  the old ones still get loaded  breaking some dependencies    There are workarounds for all of these at https   apple stackexchange com a 223163 143849   But you may be best off installing your own version of Python via the standard Python installer  Homebrew or Anaconda

User · Answer

I had the same issues   As others have mentioned  don t run pip install with sudo   Run  brew doctor    and fix the warnings and you should be able to proceed with your pip install

User · Answer

I fully agree with Mikko  but if you still want to do it  here is the way    Restart in recovery mode  Hold cmd   R  Open terminal from utilities Use the command csrutil disable

[pip] OSX El Capitan: sudo pip install OSError: [Errno: 1] Operation not permitted

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