1

Its scikit-image Download says:

pip install -U scikit-image

or

easy_install -U scikit-image

but both fail, regardless of the flag U, as shown below:

Georgioss-MacBook-Pro:Downloads gsamaras$ sudo pip install scikit-image
The directory '/Users/gsamaras/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/gsamaras/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 scikit-image
  Downloading scikit_image-0.12.3-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 (22.2MB)
    100% |████████████████████████████████| 22.2MB 53kB/s 
Requirement already satisfied: dask[array]>=0.5.0 in /Library/Python/2.7/site-packages (from scikit-image)
Collecting six>=1.7.3 (from scikit-image)
  Downloading six-1.10.0-py2.py3-none-any.whl
Collecting networkx>=1.8 (from scikit-image)
  Downloading networkx-1.11-py2.py3-none-any.whl (1.3MB)
    100% |████████████████████████████████| 1.3MB 133kB/s 
Requirement already satisfied: pillow>=2.1.0 in /Library/Python/2.7/site-packages (from scikit-image)
Requirement already satisfied: numpy; extra == "array" in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from dask[array]>=0.5.0->scikit-image)
Requirement already satisfied: toolz>=0.7.2; extra == "array" in /Library/Python/2.7/site-packages (from dask[array]>=0.5.0->scikit-image)
Collecting decorator>=3.4.0 (from networkx>=1.8->scikit-image)
  Downloading decorator-4.0.10-py2.py3-none-any.whl
Installing collected packages: six, decorator, networkx, scikit-image
  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: '/tmp/pip-qlMJKP-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six-1.4.1-py2.7.egg-info'
Georgioss-MacBook-Pro:Downloads gsamaras$

and:

Georgioss-MacBook-Pro:Downloads gsamaras$ sudo easy_install scikit-image
Searching for scikit-image
Reading https://pypi.python.org/simple/scikit-image/
Best match: scikit-image 0.12.3
Downloading https://pypi.python.org/packages/86/d0/b0192dc9a544da90f2d9150bcd84b981c6873e42a1f752b6affb89180ad8/scikit-image-0.12.3.tar.gz#md5=04ea833383e0b6ad5f65da21292c25e1
Processing scikit-image-0.12.3.tar.gz
Writing /tmp/easy_install-X6Pjoh/scikit-image-0.12.3/setup.cfg
Running scikit-image-0.12.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-X6Pjoh/scikit-image-0.12.3/egg-dist-tmp-lHJxkL
Killed: 9

Notice that brew also fails, it cannot find it.

I have Python 2.7.10, Matplotlib 1.3.1, PIL 3.4.2 and Scipy '0.18.1'. What to do?

gsamaras
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3 Answers3

5

It's generally a bad idea to install libraries on your system-wide Python. Use a virtualenv for each project instead.

First install virtualenv globally on your Mac:

$ [sudo] pip install virtualenv

Then use virtualenv command to create a new (a copy) of Python executable:

$ cd your/prefred/folder
$ virtualenv your_project

Activate the virtualenv:

$ source your_project/bin/activate

Your virtualenv is created and activated (the prompt is changed to show the activation). You can install anything in it:

$ pip install -U scikit-image
gsamaras
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Laurent LAPORTE
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  • While this should work, I would die to solve it without virtualenv. I will wait to see if something else comes by, otherwise I will accept your answer, thanks! – gsamaras Dec 06 '16 at 23:25
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    Certainly. Keep in mind that "forcing" It to be installed (using *sudo* for instance) system-wide, will pollute your Python installation and may install unwanted packages that can break your system/OS. – Laurent LAPORTE Dec 07 '16 at 06:38
  • Nothing came along. I already have installed things, it would be good to uninstall them first and then go into the virtualenv thing, right? – gsamaras Dec 07 '16 at 11:18
  • Not needed: site packages are not installed in your virtualenv (unless you specify it). – Laurent LAPORTE Dec 07 '16 at 11:53
  • Indeed, but wouldn't that be a good idea? I have posted a relevant [question](http://stackoverflow.com/questions/41017587/uninstall-all-python-packages-installed-by-me-and-their-dependencies-without-nu). See my edit! – gsamaras Dec 07 '16 at 12:55
  • When I am done executing my code, how should I close the environemnt? – gsamaras Dec 07 '16 at 13:06
2
pip install scikit-image

pip install --upgrade scikit-image

to call use skimage

Paul Roub
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Krackle
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1

(Entering this as an answer so as to include the error message). Using the first answer from @Krackle I got the following (confusing) output which I am adding here to help others:

pip install skimage
Collecting skimage
  Using cached skimage-0.0.tar.gz (757 bytes)
    ERROR: Command errored out with exit status 1:
     command: /opt/anaconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ft/7j605bsd10l0ftqygyxjjflh0000gq/T/pip-install-xtxr1328/skimage/setup.py'"'"'; __file__='"'"'/private/var/folders/ft/7j605bsd10l0ftqygyxjjflh0000gq/T/pip-install-xtxr1328/skimage/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/ft/7j605bsd10l0ftqygyxjjflh0000gq/T/pip-pip-egg-info-q8dwl8rl
         cwd: /private/var/folders/ft/7j605bsd10l0ftqygyxjjflh0000gq/T/pip-install-xtxr1328/skimage/
    Complete output (3 lines):
    
    *** Please install the `scikit-image` package (instead of `skimage`) ***
    
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I then used @Krackle's second command which (so far) has solved the problem.

peter.murray.rust
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