Not able to install scikit-image for python

[samtechbuzz]

I am having the same issue. I would appreciate the help.

Error description:

$ pip install -U scikit-image

Collecting scikit-image
Using cached scikit_image-0.13.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting matplotlib>=1.3.1 (from scikit-image)
Using cached matplotlib-2.0.2-cp35-cp35m-manylinux1_x86_64.whl
Collecting networkx>=1.8 (from scikit-image)
Using cached networkx-1.11-py2.py3-none-any.whl
Collecting scipy>=0.17.0 (from scikit-image)
Using cached scipy-0.19.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting PyWavelets>=0.4.0 (from scikit-image)
Using cached PyWavelets-0.5.2-cp35-cp35m-manylinux1_x86_64.whl
Requirement already up-to-date: six>=1.7.3 in /usr/lib/python3/dist-packages (from scikit-image)
Collecting pillow>=2.1.0 (from scikit-image)
Using cached Pillow-4.2.1-cp35-cp35m-manylinux1_x86_64.whl
Requirement already up-to-date: numpy>=1.7.1 in /home/test/.local/lib/python3.5/site-packages (from matplotlib>=1.3.1->scikit-image)
Collecting pytz (from matplotlib>=1.3.1->scikit-image)
Using cached pytz-2017.2-py2.py3-none-any.whl
Collecting pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib>=1.3.1->scikit-image)
Using cached pyparsing-2.2.0-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib>=1.3.1->scikit-image)
Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting python-dateutil (from matplotlib>=1.3.1->scikit-image)
Using cached python_dateutil-2.6.1-py2.py3-none-any.whl
Collecting decorator>=3.4.0 (from networkx>=1.8->scikit-image)
Using cached decorator-4.1.2-py2.py3-none-any.whl
Collecting olefile (from pillow>=2.1.0->scikit-image)
Installing collected packages: pytz, pyparsing, cycler, python-dateutil, matplotlib, decorator, networkx, scipy, PyWavelets, olefile, pillow, scikit-image
Found existing installation: pytz 2014.10
Uninstalling pytz-2014.10:
Exception:
Traceback (most recent call last):
File "/usr/lib/python3.5/shutil.py", line 538, in move
os.rename(src, real_dst)
PermissionError: [Errno 13] Permission denied: '/usr/lib/python3/dist-packages/pytz' -> '/tmp/pip-_gwx8g3j-uninstall/usr/lib/python3/dist-packages/pytz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/test/.local/lib/python3.5/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/home/test/.local/lib/python3.5/site-packages/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "/home/test/.local/lib/python3.5/site-packages/pip/req/req_set.py", line 778, in install
requirement.uninstall(auto_confirm=True)
File "/home/test/.local/lib/python3.5/site-packages/pip/req/req_install.py", line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File "/home/test/.local/lib/python3.5/site-packages/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/home/test/.local/lib/python3.5/site-packages/pip/utils/init.py", line 267, in renames
shutil.move(old, new)
File "/usr/lib/python3.5/shutil.py", line 550, in move
rmtree(src)
File "/usr/lib/python3.5/shutil.py", line 474, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/usr/lib/python3.5/shutil.py", line 432, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/usr/lib/python3.5/shutil.py", line 430, in _rmtree_safe_fd
os.unlink(name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'reference.py'

[pfmoore]

It looks like you're trying to upgrade a system installation (based on the fact that files are in /usr/lib/python3/dist-packages/pytz) from a non-root shell (based on the fact that your prompt is $). You shouldn't do this. You should use your distribution package manager to manage system packages, and if you want a user-managed setup, either use the --user flag for pip or use virtual environments.