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setuptools pip wheel failed with error code 2

I am going through the Google Cloud Platform's Python Bookshelf App Tutorial and I am at the step of starting up my virtualenv where I am stuck.
Running virtualenv -p python3 env produces this error:
⇒ virtualenv -p python3 env
Running virtualenv with interpreter /Library/Frameworks/Python.framework/Versions/3.6/bin/python3
Using base prefix '/Library/Frameworks/Python.framework/Versions/3.6'
New python executable in /Users/puoygae/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/bin/python3
Also creating executable in /Users/puoygae/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/bin/python
Please make sure you remove any previous custom paths from your /Users/puoygae/.pydistutils.cfg file.
Installing setuptools, pip, wheel...
Complete output from command /Users/puoygae/Lab/ga...data/env/bin/python3 - setuptools pip wheel:
Collecting setuptools
Using cached https://files.pythonhosted.org/packages/75/b3/0a106dfaf7f48aef638da80b32608617cc8de4b24a22c8cd3759c32e5d30/setuptools-41.1.0-py2.py3-none-any.whl
Collecting pip
Using cached https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl
Collecting wheel
Using cached https://files.pythonhosted.org/packages/bb/10/44230dd6bf3563b8f227dbf344c908d412ad2ff48066476672f3a72e174e/wheel-0.33.4-py2.py3-none-any.whl
Installing collected packages: setuptools, pip, wheel
Exception:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/basecommand.py", line 209, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/commands/install.py", line 317, in run
prefix=options.prefix_path,
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_set.py", line 731, in install
**kwargs
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_install.py", line 841, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_install.py", line 1040, in move_wheel_files
isolated=self.isolated,
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/wheel.py", line 343, in move_wheel_files
clobber(source, lib_dir, True)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/wheel.py", line 321, in clobber
shutil.copyfile(srcfile, destfile)
File "/Users/puoygae/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/lib/python3.6/shutil.py", line 121, in copyfile
with open(dst, 'wb') as fdst:
PermissionError: [Errno 13] Permission denied: '/lib/python3.6/site-packages/easy_install.py'
----------------------------------------
...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/virtualenv.py", line 2327, in <module>
main()
File "/Library/Python/2.7/site-packages/virtualenv.py", line 711, in main
symlink=options.symlink)
File "/Library/Python/2.7/site-packages/virtualenv.py", line 944, in create_environment
download=download,
File "/Library/Python/2.7/site-packages/virtualenv.py", line 900, in install_wheel
call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
File "/Library/Python/2.7/site-packages/virtualenv.py", line 795, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /Users/puoygae/Lab/ga...data/env/bin/python3 - setuptools pip wheel failed with error code 2
I had followed this guide to set up my python development environment. I searched the internet for a solution but I haven't had luck getting pass this step.
What is causing the issue and how can I fix it?
EDIT: Running it with sudo produces the following error:
⇒ sudo virtualenv -p python3 env
Password:
Running virtualenv with interpreter /Library/Frameworks/Python.framework/Versions/3.6/bin/python3
Using base prefix '/Library/Frameworks/Python.framework/Versions/3.6'
New python executable in /Users/myUserName/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/bin/python3
Not overwriting existing python script /Users/myUserName/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/bin/python (you must use /Users/myUserName/Lab/gae-bookshelf-app-python-flexible-experiment/getting-started-python/2-structured-data/env/bin/python3)
Please make sure you remove any previous custom paths from your /Users/myUserName/.pydistutils.cfg file.
Installing setuptools, pip, wheel...
Complete output from command /Users/myUserName/Lab/ga...data/env/bin/python3 - setuptools pip wheel:
The directory '/Users/myUserName/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/myUserName/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting setuptools
Downloading https://files.pythonhosted.org/packages/75/b3/0a106dfaf7f48aef638da80b32608617cc8de4b24a22c8cd3759c32e5d30/setuptools-41.1.0-py2.py3-none-any.whl (576kB)
Collecting pip
Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB)
Collecting wheel
Downloading https://files.pythonhosted.org/packages/bb/10/44230dd6bf3563b8f227dbf344c908d412ad2ff48066476672f3a72e174e/wheel-0.33.4-py2.py3-none-any.whl
Installing collected packages: setuptools, pip, wheel
Exception:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/basecommand.py", line 209, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/commands/install.py", line 317, in run
prefix=options.prefix_path,
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_set.py", line 731, in install
**kwargs
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_install.py", line 841, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/req/req_install.py", line 1040, in move_wheel_files
isolated=self.isolated,
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/wheel.py", line 476, in move_wheel_files
generated.extend(maker.make(spec))
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/_vendor/distlib/scripts.py", line 353, in make
self._make_script(entry, filenames, options=options)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/_vendor/distlib/scripts.py", line 257, in _make_script
self._write_script(scriptnames, shebang, script, filenames, ext)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/_vendor/distlib/scripts.py", line 231, in _write_script
self._fileop.write_binary_file(outname, script_bytes)
File "/Library/Python/2.7/site-packages/virtualenv_support/pip-8.0.2-py2.py3-none-any.whl/pip/_vendor/distlib/util.py", line 388, in write_binary_file
with open(path, 'wb') as f:
PermissionError: [Errno 1] Operation not permitted: '/bin/easy_install'
----------------------------------------
...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/virtualenv.py", line 2327, in <module>
main()
File "/Library/Python/2.7/site-packages/virtualenv.py", line 711, in main
symlink=options.symlink)
File "/Library/Python/2.7/site-packages/virtualenv.py", line 944, in create_environment
download=download,
File "/Library/Python/2.7/site-packages/virtualenv.py", line 900, in install_wheel
call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
File "/Library/Python/2.7/site-packages/virtualenv.py", line 795, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /Users/myUserName/Lab/ga...data/env/bin/python3 - setuptools pip wheel failed with error code 2

#puoygae fixed his issue by creating a new User account on his MacOS and installed python separately. The environment in his Admin account was convoluted.
Other fixes to this known issue can be :
Removing all virtualenv* things in
/usr/local/lib/python2.7/dist-packages/ and reinstalling it as per
this GitHub issue.
Uninstall any setuptools and wheels from pip. Also uninstall them
from the apt-get remove wheel setuptools virutalenv(if they exist,
In some cases wheels and setuptools both can exist and may conflict
with each other from pip and apt-get installations) > Download fresh
setuptools-35.0.2 from here and virutalenv-15.1.0 from here.
Install both the tools freshly.
Follow the instructions on updating openSSL here and then try
setting up a virtual environment using pip install.
Could try to open the system terminal and type pip install
virtualenv. Restart IDE.
Try installing pysocks - sudo pip install pysocks Use - unset
all_proxy Retry
Also you can try upgrading to platformio-ide 2.1.5
"setenv all_proxy https://proxy_here:port_here/". Solves the proxy
problem for not only this setup but for all installations.
Also have a look at this stackoverflow thread fixes for the
same issue.
Reference Links :
https://github.com/platformio/platformio-atom-ide/issues/1245
https://github.com/pypa/virtualenv/issues/876

I had this problem as well.
My pip was looking at a different repo, the one I created using AWS's CodeArtifact, which needs login and credentials.
In my case, all I needed to do was erase this file ~/.config/pip/pip.config

panda install error on mac because of existing numpy

I installed pip to my MacBook Air manually by sudo python get-pip.py.
and have tried to install pandas by sudo -Hi pip install pandas but got this:
(Note: I checked the other similar questions but my problem is different.)
$ sudo -Hi pip install pandas
Collecting pandas
Using cached pandas-0.22.0-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
Requirement already satisfied: python-dateutil in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas)
Collecting numpy>=1.9.0 (from pandas)
Using cached numpy-1.14.0-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
Requirement already satisfied: pytz>=2011k in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas)
Installing collected packages: numpy, pandas
Found existing installation: numpy 1.8.0rc1
DEPRECATION: Uninstalling a distutils installed project (numpy) 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 numpy-1.8.0rc1:
Exception:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "/Library/Python/2.7/site-packages/pip/req/req_set.py", line 778, in install
requirement.uninstall(auto_confirm=True)
File "/Library/Python/2.7/site-packages/pip/req/req_install.py", line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File "/Library/Python/2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/Library/Python/2.7/site-packages/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: '/tmp/pip-FbYaYw-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'
How can I fix this?

Error while installing core ML tools [duplicate]

This question already has answers here:
Error installing coremltools
(5 answers)
Closed 5 years ago.
I am trying to convert a caffe model to core ML model.
Please find the error while running pip install coremltools
Collecting coremltools
Using cached coremltools-0.4.0-py2.7-none-any.whl
Requirement already satisfied: numpy>=1.6.2 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from coremltools)
Collecting protobuf>=3.1.0 (from coremltools)
Using cached protobuf-3.3.0.tar.gz
Collecting six>=1.9 (from protobuf>=3.1.0->coremltools)
Using cached six-1.10.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from protobuf>=3.1.0->coremltools)
Installing collected packages: six, protobuf, coremltools
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-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 778, in install
requirement.uninstall(auto_confirm=True)
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/5z/5hfw98ks677_r5rqm498kq1c0000gn/T/pip-DMhcCb-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six-1.4.1-py2.7.egg-info'
I am new to machine learning. Please suggest a solution

As error said - operation is not permitted. I'm Linux not Mac user - but it's probably because you try to do this without root privilages.
You can try sudo pip install coremltools. But generally speaking installing development libraries system-wide is not best practice.
You should definitely use virtualenv.

PermissionError: [Errno 13] Permission denied: 'C:\\Program Files\\Python35\\Lib\\site-packages\\six.py'

I am using python 3.5.3, and now I want to install pandas and numpy but not able to, following is the error in cmd, anyone can help me?
C:\Program Files\Python35\Scripts>py -3.5 -m pip install pandas
Collecting pandas
Using cached pandas-0.20.1-cp35-cp35m-win_amd64.whl
Collecting python-dateutil>=2 (from pandas)
Using cached python_dateutil-2.6.0-py2.py3-none-any.whl
Collecting numpy>=1.7.0 (from pandas)
Using cached numpy-1.12.1-cp35-none-win_amd64.whl
Collecting pytz>=2011k (from pandas)
Using cached pytz-2017.2-py2.py3-none-any.whl
Collecting six>=1.5 (from python-dateutil>=2->pandas)
Using cached six-1.10.0-py2.py3-none-any.whl
Installing collected packages: six, python-dateutil, numpy, pytz, pandas
Exception:
Traceback (most recent call last):
File "C:\Program Files\Python35\lib\site-packages\pip\basecommand.py", line 215, in main
status = self.run(options, args)
File "C:\Program Files\Python35\lib\site-packages\pip\commands\install.py", line 342, in run
prefix=options.prefix_path,
File "C:\Program Files\Python35\lib\site-packages\pip\req\req_set.py", line 784, in install
**kwargs
File "C:\Program Files\Python35\lib\site-packages\pip\req\req_install.py", line 851, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File "C:\Program Files\Python35\lib\site-packages\pip\req\req_install.py", line 1064, in move_wheel_files
isolated=self.isolated,
File "C:\Program Files\Python35\lib\site-packages\pip\wheel.py", line 345, in move_wheel_files
clobber(source, lib_dir, True)
File "C:\Program Files\Python35\lib\site-packages\pip\wheel.py", line 323, in clobber
shutil.copyfile(srcfile, destfile)
File "C:\Program Files\Python35\lib\shutil.py", line 121, in copyfile
with open(dst, 'wb') as fdst:
PermissionError: [Errno 13] Permission denied: 'C:\\Program Files\\Python35\\Lib\\site-packages\\six.py'

As others have pointed out you need to run the command with admin privileges.
How to do this varies by windows version, but on Windows 8 and 10 you can just press Windows+X (or just right-clicking the Start button). On the menu, choose “Command Prompt (Admin).”

The command line you're using does not have access to C:\\Program Files\\Python35\\Lib\\site-packages\\six.py.
Run the command in a command line with administrative priveleges.

Run command line in admin mode and then :
pip instal pandas

unable to install Boto3 on windows

I am getting below exception after running pip install boto3 command
C:\boto3-develop>pip install boto3
Collecting boto3
Downloading boto3-1.4.4-py2.py3-none-any.whl (127kB)
100% |████████████████████████████████| 133kB 281kB/s
Collecting jmespath<1.0.0,>=0.7.1 (from boto3)
Downloading jmespath-0.9.2-py2.py3-none-any.whl
Collecting s3transfer<0.2.0,>=0.1.10 (from boto3) Downloading
s3transfer-0.1.10-py2.py3-none-any.whl (54kB)
100% |████████████████████████████████| 61kB 787kB/s
Collecting botocore<1.6.0,>=1.5.0 (from boto3) Downloading
botocore-1.5.26-py2.py3-none-any.whl (3.4MB)
100% |████████████████████████████████| 3.4MB 81kB/s
Collecting docutils>=0.10 (from botocore<1.6.0,>=1.5.0->boto3)
Downloading docutils-0.13.1-py3-none-any.whl (536kB)
100% |████████████████████████████████| 542kB 205kB/s
Collecting python-dateutil<3.0.0,>=2.1 (from
botocore<1.6.0,>=1.5.0->boto3) Downloading
python_dateutil-2.6.0-py2.py3-none-any.whl (194kB)
100% |████████████████████████████████| 194kB 273kB/s
Collecting six>=1.5 (from
python-dateutil<3.0.0,>=2.1->botocore<1.6.0,>=1.5.0->b oto3)
Downloading six-1.10.0-py2.py3-none-any.whl
Installing collected packages: jmespath, docutils, six,
python-dateutil, botocor e, s3transfer, boto3
Exception: Traceback (most recent call last): File "c:\program files
(x86)\python36-32\lib\site-packages\pip\basecommand.py" , line 215, in
main
status = self.run(options, args)
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\commands\instal l.py", line
342, in run
prefix=options.prefix_path,
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\req\req_set.py" , line 784, in
install
**kwargs
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\req\req_install .py", line
851, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\req\req_install .py", line
1064, in move_wheel_files
isolated=self.isolated,
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\wheel.py", line 345, in
move_wheel_files
clobber(source, lib_dir, True)
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\wheel.py", line 316, in
clobber
ensure_dir(destdir)
File "c:\program files
(x86)\python36-32\lib\site-packages\pip\utils__init__. py", line 83,
in ensure_dir
os.makedirs(path)
File "c:\program files (x86)\python36-32\lib\os.py", line 220, in
makedirs
mkdir(name, mode)
PermissionError: [WinError 5] Access is denied: 'c:\program files
(x86)\python 36-32\Lib\site-packages\jmespath'
C:\boto3-develop>

Make sure you are running the command line as administrator. Lack of privileges often prevents installation of python packages.