Unable to Update jupyter via PIP on Mac

[Mihkael Kolodny]

Hi All - Appreciate your assistance in advance. I am trying to install Jupyter and I am having issues installing dependencies. Can you please assist me with troubleshooting?

I ran the command:

sudo -H python -m pip install jupyter

Output:

Collecting jupyter

  Using cached jupyter-1.0.0-py2.py3-none-any.whl

Collecting jupyter-console (from jupyter)

  Using cached jupyter_console-5.2.0-py2.py3-none-any.whl

Requirement already satisfied: ipykernel in /Library/Python/2.7/site-packages (from jupyter)

Collecting notebook (from jupyter)

  Using cached notebook-5.2.2-py2.py3-none-any.whl

Collecting nbconvert (from jupyter)

  Using cached nbconvert-5.3.1-py2.py3-none-any.whl

Collecting qtconsole (from jupyter)

  Using cached qtconsole-4.3.1-py2.py3-none-any.whl

Collecting ipywidgets (from jupyter)

  Using cached ipywidgets-7.0.5-py2.py3-none-any.whl

Requirement already satisfied: jupyter-client in /Library/Python/2.7/site-packages (from jupyter-console->jupyter)

Requirement already satisfied: ipython in /Library/Python/2.7/site-packages (from jupyter-console->jupyter)

Requirement already satisfied: pygments in /Library/Python/2.7/site-packages (from jupyter-console->jupyter)

Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.0 in /Library/Python/2.7/site-packages (from jupyter-console->jupyter)

Requirement already satisfied: tornado>=4.0 in /Library/Python/2.7/site-packages (from ipykernel->jupyter)

Requirement already satisfied: traitlets>=4.1.0 in /Library/Python/2.7/site-packages (from ipykernel->jupyter)

Collecting terminado>=0.3.3; sys_platform != "win32" (from notebook->jupyter)

  Using cached terminado-0.8.1-py2.py3-none-any.whl

Requirement already satisfied: ipython-genutils in /Library/Python/2.7/site-packages (from notebook->jupyter)

Collecting jinja2 (from notebook->jupyter)

  Using cached Jinja2-2.10-py2.py3-none-any.whl

Requirement already satisfied: jupyter-core in /Library/Python/2.7/site-packages (from notebook->jupyter)

Collecting nbformat (from notebook->jupyter)

  Using cached nbformat-4.4.0-py2.py3-none-any.whl

Collecting mistune>=0.7.4 (from nbconvert->jupyter)

  Using cached mistune-0.8.3-py2.py3-none-any.whl

Collecting bleach (from nbconvert->jupyter)

  Using cached bleach-2.1.2-py2.py3-none-any.whl

Collecting testpath (from nbconvert->jupyter)

  Using cached testpath-0.3.1-py2.py3-none-any.whl

Collecting pandocfilters>=1.4.1 (from nbconvert->jupyter)

  Using cached pandocfilters-1.4.2.tar.gz

Collecting entrypoints>=0.2.2 (from nbconvert->jupyter)

  Using cached entrypoints-0.2.3-py2.py3-none-any.whl

Collecting widgetsnbextension~=3.0.0 (from ipywidgets->jupyter)

  Using cached widgetsnbextension-3.0.8-py2.py3-none-any.whl

Requirement already satisfied: pyzmq>=13 in /Library/Python/2.7/site-packages (from jupyter-client->jupyter-console->jupyter)

Requirement already satisfied: python-dateutil>=2.1 in /Library/Python/2.7/site-packages (from jupyter-client->jupyter-console->jupyter)

Requirement already satisfied: setuptools>=18.5 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from ipython->jupyter-console->jupyter)

Requirement already satisfied: simplegeneric>0.8 in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Collecting backports.shutil-get-terminal-size; python_version == "2.7" (from ipython->jupyter-console->jupyter)

  Using cached backports.shutil_get_terminal_size-1.0.0-py2.py3-none-any.whl

Requirement already satisfied: appnope; sys_platform == "darwin" in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Requirement already satisfied: pexpect; sys_platform != "win32" in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Requirement already satisfied: pickleshare in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Requirement already satisfied: decorator in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /Library/Python/2.7/site-packages (from ipython->jupyter-console->jupyter)

Requirement already satisfied: wcwidth in /Library/Python/2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.0->jupyter-console->jupyter)

Requirement already satisfied: six>=1.9.0 in /Library/Python/2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.0->jupyter-console->jupyter)

Requirement already satisfied: singledispatch in /Library/Python/2.7/site-packages (from tornado>=4.0->ipykernel->jupyter)

Requirement already satisfied: certifi in /Library/Python/2.7/site-packages (from tornado>=4.0->ipykernel->jupyter)

Requirement already satisfied: backports_abc>=0.4 in /Library/Python/2.7/site-packages (from tornado>=4.0->ipykernel->jupyter)

Collecting enum34; python_version == "2.7" (from traitlets>=4.1.0->ipykernel->jupyter)

  Using cached enum34-1.1.6-py2-none-any.whl

Requirement already satisfied: ptyprocess; os_name != "nt" in /Library/Python/2.7/site-packages (from terminado>=0.3.3; sys_platform != "win32"->notebook->jupyter)

Collecting MarkupSafe>=0.23 (from jinja2->notebook->jupyter)

  Using cached MarkupSafe-1.0.tar.gz

Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /Library/Python/2.7/site-packages (from nbformat->notebook->jupyter)

Collecting html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre (from bleach->nbconvert->jupyter)

  Using cached html5lib-1.0.1-py2.py3-none-any.whl

Collecting configparser>=3.5; python_version == "2.7" (from entrypoints>=0.2.2->nbconvert->jupyter)

  Using cached configparser-3.5.0.tar.gz

Requirement already satisfied: scandir; python_version < "3.5" in /Library/Python/2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython->jupyter-console->jupyter)

Requirement already satisfied: functools32; python_version == "2.7" in /Library/Python/2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->notebook->jupyter)

Collecting webencodings (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->jupyter)

  Using cached webencodings-0.5.1-py2.py3-none-any.whl

Installing collected packages: jupyter-console, terminado, MarkupSafe, jinja2, mistune, nbformat, webencodings, html5lib, bleach, testpath, pandocfilters, configparser, entrypoints, nbconvert, notebook, qtconsole, widgetsnbextension, ipywidgets, jupyter, backports.shutil-get-terminal-size, enum34

  Running setup.py install for MarkupSafe ... done

  Running setup.py install for pandocfilters ... done

  Running setup.py install for configparser ... done

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 377, in move_wheel_files

    clobber(source, dest, False, fixer=fixer, filter=filter)

  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/wheel.py", line 316, in clobber

    ensure_dir(destdir)

  File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py", line 83, in ensure_dir

    os.makedirs(path)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 150, in makedirs

    makedirs(head, mode)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 150, in makedirs

    makedirs(head, mode)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 150, in makedirs

    makedirs(head, mode)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs

    mkdir(name, mode)

OSError: [Errno 1] Operation not permitted: '/System/Library/Frameworks/Python.framework/Versions/2.7/share' 

[Thomas Kluyver]

It's not recommended to use pip with sudo. Either user the --user flag for pip to install under your home directory, or create a virtualenv or conda env to install packages into.

Thomas

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[M Pacer]

To say a bit more, the issues you are running into are potentially related to permission issues that stem from you installing with sudo. It will be hard to help you more specifically until we know for sure that it does not stem from your using sudo. 

Here's a link to conda: https://conda.io/docs/download.html. I would recommend that you install miniconda rather than anaconda. If you did install using miniconda, you would then want to create a virtual environment (conda create -n my_virtual_environment python=3) switch to that environment (source activate my_virtual_environment) and then install Jupyter in that environment (conda install jupyter).

Unfortunately, I don't know of the best link to get started with virtualenv. But others may chime in if you don't want to use conda.

NB: none of those commands use sudo!

Cheers,

M

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[Matthias Bussonnier]

On 15 December 2017 at 19:55, M Pacer <mpa...@berkeley.edu> wrote:

To say a bit more, the issues you are running into are potentially related to permission issues that stem from you installing with sudo. It will be hard to help you more specifically until we know for sure that it does not stem from your using sudo. 

I even think this is due to apple System Integrity Protection[1], this makes part of the macOS  filesytem read-only because you should really, really, really not change these files/directories. One of the reasons to SIP introduction was abuse of sudo to install software. As an example changing System/Library/Frameworks/Python.framework/Versions/2.7/share is likely to make your mac unbootable either now, or at next system update. SIP cannot be disabled (IIRC) without rebooting your mac in single user mode.

-- 

Matthias

1: https://en.wikipedia.org/wiki/System_Integrity_Protection

[Lawrence D’Oliveiro]

On Saturday, December 16, 2017 at 8:15:10 AM UTC+13, Matthias Bussonnier wrote:

I even think this is due to apple System Integrity Protection[1], this makes part of the macOS  filesytem read-only because you should really, really, really not change these files/directories. One of the reasons to SIP introduction was abuse of sudo to install software. As an example changing System/Library/Frameworks/Python.framework/Versions/2.7/share is likely to make your mac unbootable either now, or at next system update. SIP cannot be disabled (IIRC) without rebooting your mac in single user mode.

Doesn’t macOS have the concept of /usr/local? I thought that was a standard Unix thing.