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Permission error with pip Python 3

I am using Python 3 on Mac OS X. Everything was perfect, I used to install packages like this:
pip install somePackage
But IDLE stopped working so I had to re-install it. After that, when I ran pip, I got pip is not defined so I had to install pip. Now, every time I try to install a package using pip, I get this error:
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 287, in clobber
ensure_dir(dest) # common for the 'include' path
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 157, in makedirs
mkdir(name, mode)
OSError: [Errno 1] Operation not permitted: '/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/pygame'
I thought it may be from the version so I updated it. Now, whenever I run pip install something I get this error:
Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/bc/hwpn9sqn5352xcbst0p89snm0000gn/T/pip-build-hSNyxK/termcolor/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /var/folders/bc/hwpn9sqn5352xcbst0p89snm0000gn/T/pip-U3ZtNq-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/bc/hwpn9sqn5352xcbst0p89snm0000gn/T/pip-build-hSNyxK/termcolor/
I can't even delete a package - when I run pip uninstall something I get this error:
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/uninstall.py", line 76, in run
requirement_set.uninstall(auto_confirm=options.yes)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py", line 346, in uninstall
req.uninstall(auto_confirm=auto_confirm)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py", line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py", line 267, 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/bc/hwpn9sqn5352xcbst0p89snm0000gn/T/pip-OQKY_a-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'
My pip version is :
pip 9.0.1 from /Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg (python 2.7)
I am using Mac 10.12.6
How can I fix this?

The permission error you're seeing is due to the fact that your site-packages directory (where pip is trying to install to) is protected and owned by an administrator.
Where is the site packages directory
It depends on your Python distribution. That's why I asked for you to include the output of the $ which python command (from the command line), and the >>> import site; site.getsitepackages() command (from Python). These will help you figure out where your site packages directory is. Also, running pip -v will print the directory to which pip is trying to install.
It is important to note that Macs come with a system version of Python. You should not install any packages accessible to this system version of Python, because it is used by the system and you can potentially interfere with its normal workings and/or install malicious versions of packages that will do bad things when the system uses that Python (e.g., if someone made a nasty egg and called it "os" and put it in the site-packages directory for your system Python, then the next time the system python version ran "import os" it would import the nasty egg.)
Why overriding with sudo pip install is not a good solution
While running your pip install command as sudo would probably solve the problem, this is a short-term fix that is very bad for the reasons mentioned in my comment in #Nenand's answer - running pip install X downloads the egg for X from the internet, and runs python setup.py build && python setup.py install on whatever happens to be in the setup.py. While it's easy to be lulled into complacency because, hey, it works!, it's also naive to trust strangers on the internet (and let's face it, the people who make pip packages are strangers to you).
EDIT: I didn't even think of this, but there is also the potential that you mis-type a library, or guess the wrong name, and end up with one you REALLY didn't want (typosquatting). See this BleepingComputer article on typosquatting pip packages.
The proper solution
The proper solution is to figure out why your site-packages directory is protected, and either fix its permissions, or change the site-packages directory pip is using.
I suspect the reason you're seeing this permissions error is that pip is trying to install to the system Python's site-packages directory, which is owned by root for a good reason. The system Python is located at /usr/bin/ and its site-packages directory is located at the following directories:
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages'
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/site-python'
'/Library/Python/2.7/site-packages'
My advice, in this case, is to install Python using Homebrew, Python.org, or Canopy, which will keep your snakes in separate cages and will leave the system Python alone. On my system, python is the system python, python2 is Python version 2, and python3 is Python version 3. This also makes it more clear which version I'm using. I also do not have a pip command - not on my path - so I can't accidentally install something to my system Python. I have to explicitly call pip2 or pip3. Using Homebrew Python will do all of this for you, so that's my most-favored recommendation of the many Python distributions available.

Proper installation of Python 3.6 on Ubuntu 14.06 to include IDLE

I am trying to install Python 3.6 on Ubuntu 14.06. I have tried the get-apt command and I have tried to install from a tarball. Either way this is the error I receive.
:~/Downloads$ pip install Python-43.4.6.tar.gz
Requirement 'Python-43.4.6.tar.gz' looks like a filename, but the file does not exist
Processing ./Python-43.4.6.tar.gz
Exception: Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 209, in main status = self.run(options, args)
File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 328, in run wb.build(autobuilding=True)
File "/usr/lib/python2.7/dist-packages/pip/wheel.py", line 748, in build self.requirement_set.prepare_files(self.finder)
File "/usr/lib/python2.7/dist-packages/pip/req/req_set.py", line 360, in prepare_files ignore_dependencies=self.ignore_dependencies))
File "/usr/lib/python2.7/dist-packages/pip/req/req_set.py", line 577, in _prepare_file session=self.session, hashes=hashes)
File "/usr/lib/python2.7/dist-packages/pip/download.py", line 798, in unpack_url unpack_file_url(link, location, download_dir, hashes=hashes) File "/usr/lib/python2.7/dist-packages/pip/download.py", line 705, in unpack_file_url unpack_file(from_path, location, content_type, link) File "/usr/lib/python2.7/dist-packages/pip/utils/__init__.py", line 620, in unpack_file tarfile.is_tarfile(filename) or
File "/usr/lib/python2.7/tarfile.py", line 2622, in is_tarfile t = open(name)
File "/usr/lib/python2.7/tarfile.py", line 1673, in open return func(name, "r", fileobj, **kwargs)
File "/usr/lib/python2.7/tarfile.py", line 1738, in gzopen fileobj = gzip.GzipFile(name, mode, compresslevel, fileobj)
File "/usr/lib/python2.7/gzip.py", line 94, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: '/home/michael/Downloads/Python-43.4.6.tar.gz'
You are using pip version 8.1.1, however version 9.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.
:~/Downloads$ pip install --upgrade pip
Collecting pip
Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) 100% |████████████████████████████████| 1.3MB 662kB/s Installing collected packages: pip
Successfully installed pip-8.1.1
You are using pip version 8.1.1, however version 9.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.
~/Downloads$ pip -V
pip 9.0.1 from /home/michael/.local/lib/python2.7/site-packages (python 2.7)
~/Downloads$ python -V
Python 2.7.12
~/Downloads$ python3 -V
Python 3.5.2
Did I download the wrong tarball or is there a way to insure that I am not install with for Python 2.7? Also, is the pip version error related?
TIA

First try using the upgrade command in pip and see if that fixes the version problem
pip3 install --upgrade pip
otherwise I would recommend uninstalling and performing a fresh install.
Use the following commands to setup python
sudo apt-get update
sudo apt-get -y upgrade
sudo apt-get install python3.6 python3-pip idle3
pip3 install numpy
pip3 install spyder
pip3 is the command for using python installer for python3.
to use idle3, just type in into the command window
idle3
I suggest to install spyder using pip3 as spyder is a more advanced idle which can track variables and code writing. makes it a bit easier in locating errors and such.

Many linux distribution provide tkinter, IDLE (which uses tkinter), and turtle (which also uses tkinter) as separate distribution. Searching SO for [tkinter] install tkinter on ubuntu displays previous questions with answers.
sudo apt-get install python3-tk
may be what you need but details may have change since previous answers.

pip uninstall working but giving error

I have downloaded, built and installed the sample pypi project. The project is supposed to be used to give an insight to python packaging and is referenced in Python Packaging User Guide and Packaging and Distributing Projects. I am therefore confused to why on earth following their instructions on creating the package I have an error when uninstalling it.
As mentioned above I have used their sample project. If anyone can shed some light it would be appreciated.
Key notes: I am running Mac OSX, my installed python version is 3.5.1
Below are steps to reproduce the problem:
mkdir testdirectory
cd testdirectory/
pyvenv venv # Creating a virtual environment
source venv/bin/activate
git clone https://github.com/pypa/sampleproject.git # Getting sample project
cd sampleproject/
python setup.py build
python setup.py install # Installing on the virtual environment
pip list
peppercorn (0.5)
pip (7.1.2)
sample (1.2.0)
setuptools (18.2)
pip uninstall sample
Resulting in the following output:
Uninstalling sample-1.2.0:
/Users/steve/testdirectory/venv/bin/sample
/Users/steve/testdirectory/venv/lib/python3.5/site-packages/sample-1.2.0-py3.5.egg
Proceed (y/n)? y
Successfully uninstalled sample-1.2.0
Traceback (most recent call last):
File "/Users/steve/testdirectory/venv/bin/pip3", line 11, in <module>
sys.exit(main())
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/__init__.py", line 217, in main
return command.main(cmd_args)
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/basecommand.py", line 248, in main
pip_version_check(session)
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/utils/outdated.py", line 102, in pip_version_check
installed_version = get_installed_version("pip")
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/utils/__init__.py", line 858, in get_installed_version
working_set = pkg_resources.WorkingSet()
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 629, in __init__
self.add_entry(entry)
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 685, in add_entry
for dist in find_distributions(entry, True):
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2075, in find_eggs_in_zip
if metadata.has_metadata('PKG-INFO'):
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1605, in has_metadata
return self.egg_info and self._has(self._fn(self.egg_info, name))
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1963, in _has
return zip_path in self.zipinfo or zip_path in self._index()
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1843, in zipinfo
return self._zip_manifests.load(self.loader.archive)
File "/Users/steve/testdirectory/venv/lib/python3.5/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1783, in load
mtime = os.stat(path).st_mtime
FileNotFoundError: [Errno 2] No such file or directory: '/Users/steve/testdirectory/venv/lib/python3.5/site-packages/sample-1.2.0-py3.5.egg'
It appears that the package has uninstalled correctly however the error is still thrown.

This is documented:
$ pip help uninstall
Usage:
pip uninstall [options] <package> ...
pip uninstall [options] -r <requirements file> ...
Description:
Uninstall packages.
pip is able to uninstall most installed packages. Known exceptions are:
- Pure distutils packages installed with ``python setup.py install``, which
leave behind no metadata to determine what files were installed.
- Script wrappers installed by ``python setup.py develop``.
i.e. you are getting the error because you didn't use pip itself to install - you used setup.py and so pip doesn't know what was installed.

Install package not with python setup.py install but with pip install .
Then uninstalling will work without errors

Manually installing python dependencies doesn't work. Why?

Whenever I install my python project using 'python setup.py install', and invoke my project on a CentOS vagrant box, it works great. The dependencies get resolved perfectly.
However, if I create an rpm using fpm for my project, install the rpm using 'rpm -i rpm-file.rpm', manually install the dependencies using 'pip install -r requirements-file-path.txt' and then invoke my project on another CentOS vagrant box, I get the following error:
File "/usr/bin/<name-of-my-project>", line 5, in <module>
from pkg_resources import load_entry_point
File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 2655, in <module>
working_set.require(__requires__)
File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 648, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 546, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: fabric==1.10.2
Uninstalling the dependencies using 'pip uninstall' and reinstalling them doesn't fix the problem. What am I missing?

Just found the answer on the Fabric FAQ page: http://www.fabfile.org/faq.html/. Executing:
sudo pip install -U setuptools
Then re-installing the dependencies and project solved my problem. But welcome to other answers.

Exception Error when Installing NumPy with pip

I have been trying to install NumPy and have been have a brutal time with it. I keep getting an exception error no matter what I try. I used the command
$pip install numpy
but it threw this error
Exception:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/basecommand.py", line 246, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/commands/install.py", line 352, in run
root=options.root_path,
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/req/req_set.py", line 693, in install
**kwargs
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/req/req_install.py", line 817, in install
self.move_wheel_files(self.source_dir, root=root)
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/req/req_install.py", line 1018, in move_wheel_files
isolated=self.isolated,
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/wheel.py", line 269, in move_wheel_files
clobber(source, dest, False, fixer=fixer, filter=filter)
File "/Library/Python/2.7/site-packages/pip-6.1.1-py2.7.egg/pip/wheel.py", line 215, in clobber
shutil.copyfile(srcfile, destfile)
File "/usr/local/Cellar/python/2.7.9/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: '/usr/local/man/man1/nosetests.1'
Just to check, I used import in Python to see if it got anything, it also threw an error though. I have no idea what is going on.
$pip install scipy
gave me no problems. Any help is appreciated! I can't seem to find anything on how to fix this.
Thanks!

Homebrew tries to leave /usr/local writable, so you don't need sudo. See the FAQ for details.
However, if you accidentally use sudo once—or if some other installer you run installs stuff into /usr/local that doesn't realize you wanted it Homebrew-style—then you'll start getting errors, when your Homebrew stuff attempt to modify files that were saved with sudo.
There's a particular problem if you try to use both Apple's pre-installed Python 2.7 and a Homebrew Python 2.7: they both want to install scripts to /usr/local/bin, man pages to /usr/local/man, etc. And Apple's wants to use sudo.
So, most likely, you did a sudo pip install nose for Apple's Python in the past, and now pip install nose for Homebrew's Python is trying to overwrite its files and doesn't have permissions to do so. (Or maybe not nose itself, but something else that requires nose without you realizing it.)
Using sudo with the Homebrew Python will just make the problem worse; don't do that.
The right solution is to either:
Not use a third-party Python 2.7, Homebrew or otherwise, and just stick with Apple's (or upgrade to Python 3; then there's usually no conflict with Apple's 2.7…), or
Never touch Apple's Python 2.7, and only use the other one.
But at this point, you've already screwed things up, and I doubt you want to reinstall your OS from scratch, right?
You can fix things by brew uninstall python for the former, or by uninstalling everything you installed with Apple's Python for the latter. (You can't uninstall Apple's Python; that would break the OS, and the next OS update would just undo it anyway…) And then, either way, you'll probably want to reinstall every package you need for whichever Python you chose to go with, to be safe.
Or, for a quick&dirty solution, every time you get an error like this, you can either delete the conflicting file (sudo rm /usr/local/man/man1/nosetests.1) or make it overwritable (sudo chmod a+w /usr/local/man/man1/nosetests.1); then, your pip will work. Until the next error, which you can fix the same way.

Just run cmd as Admin it worked for me.