# Error when installing scikit-image via Python Interactor

**URL:** <https://discourse.slicer.org/t/error-when-installing-scikit-image-via-python-interactor/2253>\
**Category:** Development\
**Tags:** segmentation, python\
**Created:** [March 6, 2018, 10:13pm UTC](https://discourse.slicer.org/t/error-when-installing-scikit-image-via-python-interactor/2253 "2018-03-06T22:13:25Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![ckuzi001](https://avatars.discourse-cdn.com/v4/letter/c/c67d28/32.png) [@ckuzi001](https://discourse.slicer.org/u/ckuzi001)\
**Post date:** [March 6, 2018, 10:13pm UTC](https://discourse.slicer.org/t/error-when-installing-scikit-image-via-python-interactor/2253/1 "2018-03-06T22:13:26Z")

</div>

Hello Everyone,

I am attempting to install the scikit-image package via the Slicer Python Interactor using the command:

> > > pip.main([‘install’, ‘scikit-image’])

However, this throws an error. As a test, I tried the same command using other packages, including scikit-learn.

> > > pip.main([‘install’, ‘scikit-learn’])

This worked without any errors. The version I am running is 3D Slicer 4.8.1/Python 2.7 on Ubuntu. Any assistance resolving this issue would be greatly appreciated.

Thank you,

~ Carrie

PS – I’ve copied and pasted the output below.

```auto
----------------------------------------------------------------------------------------------------

Collecting scikit-image
  Using cached scikit_image-0.13.1-cp27-cp27m-manylinux1_x86_64.whl
Collecting matplotlib>=1.3.1 (from scikit-image)
  Using cached matplotlib-2.2.0-cp27-cp27m-manylinux1_x86_64.whl
Requirement already up-to-date: six>=1.7.3 in ./lib/Python/lib/python2.7/site-packages (from scikit-image)
Collecting networkx>=1.8 (from scikit-image)
  Using cached networkx-2.1.zip
Collecting pillow>=2.1.0 (from scikit-image)
  Using cached Pillow-5.0.0-cp27-cp27m-manylinux1_x86_64.whl
Collecting PyWavelets>=0.4.0 (from scikit-image)
  Using cached PyWavelets-0.5.2-cp27-cp27m-manylinux1_x86_64.whl
Requirement already up-to-date: scipy>=0.17.0 in ./lib/Python/lib/python2.7/site-packages (from scikit-image)
Requirement already up-to-date: python-dateutil>=2.1 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already up-to-date: cycler>=0.10 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Collecting subprocess32 (from matplotlib>=1.3.1->scikit-image)
  Using cached subprocess32-3.2.7.tar.gz
Collecting pytz (from matplotlib>=1.3.1->scikit-image)
  Using cached pytz-2018.3-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib>=1.3.1->scikit-image)
  Using cached backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Collecting numpy>=1.7.1 (from matplotlib>=1.3.1->scikit-image)
  Using cached numpy-1.14.1-cp27-cp27m-manylinux1_x86_64.whl
Collecting kiwisolver>=1.0.1 (from matplotlib>=1.3.1->scikit-image)
  Using cached kiwisolver-1.0.1-cp27-cp27m-manylinux1_x86_64.whl
Collecting decorator>=4.1.0 (from networkx>=1.8->scikit-image)
  Using cached decorator-4.2.1-py2.py3-none-any.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib>=1.3.1->scikit-image)
  Using cached setuptools-38.5.2-py2.py3-none-any.whl
Building wheels for collected packages: networkx, subprocess32
  Running setup.py bdist_wheel for networkx: started
  Running setup.py bdist_wheel for networkx: finished with status 'error'
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/networkx/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" bdist_wheel -d /tmp/tmpbIzR__pip-wheel- --python-tag cp27:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed building wheel for networkx
  Running setup.py clean for networkx
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/networkx/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" clean --all:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed cleaning build dir for networkx
  Running setup.py bdist_wheel for subprocess32: started
  Running setup.py bdist_wheel for subprocess32: finished with status 'error'
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" bdist_wheel -d /tmp/tmpYZu52jpip-wheel- --python-tag cp27:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed building wheel for subprocess32
  Running setup.py clean for subprocess32
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" clean --all:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed cleaning build dir for subprocess32
Failed to build networkx subprocess32
Installing collected packages: subprocess32, pytz, backports.functools-lru-cache, numpy, setuptools, kiwisolver, matplotlib, decorator, networkx, pillow, PyWavelets, scikit-image
  Running setup.py install for subprocess32: started
    Running setup.py install for subprocess32: finished with status 'error'
    Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" install --record /tmp/pip-f8oqVV-record/install-record.txt --single-version-externally-managed --compile:
    usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: --help [cmd1 cmd2 ...]
       or: --help-commands
       or: cmd --help
    
    error: option -u not recognized
    
    ----------------------------------------
Command ""/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-eE_lIS/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" install --record /tmp/pip-f8oqVV-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-eE_lIS/subprocess32/
1
>>> pip.main(['install', 'numpy'])
Requirement already satisfied: numpy in ./lib/Python/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg
0
>>> pip.main(['install', 'skimage'])
Collecting skimage
  Downloading skimage-0.0.tar.gz
    Complete output from command python setup.py egg_info:
    
    ***Please install the `scikit-image` package (instead of `skimage`)***
    
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-PINFjC/skimage/
1
>>> pip.main(['install', 'scikit-image'])
Collecting scikit-image
  Using cached scikit_image-0.13.1-cp27-cp27m-manylinux1_x86_64.whl
Collecting matplotlib>=1.3.1 (from scikit-image)
  Using cached matplotlib-2.2.0-cp27-cp27m-manylinux1_x86_64.whl
Requirement already satisfied: six>=1.7.3 in ./lib/Python/lib/python2.7/site-packages (from scikit-image)
Collecting networkx>=1.8 (from scikit-image)
  Using cached networkx-2.1.zip
Collecting pillow>=2.1.0 (from scikit-image)
  Using cached Pillow-5.0.0-cp27-cp27m-manylinux1_x86_64.whl
Collecting PyWavelets>=0.4.0 (from scikit-image)
  Using cached PyWavelets-0.5.2-cp27-cp27m-manylinux1_x86_64.whl
Requirement already satisfied: scipy>=0.17.0 in ./lib/Python/lib/python2.7/site-packages (from scikit-image)
Requirement already satisfied: python-dateutil>=2.1 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: cycler>=0.10 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Collecting subprocess32 (from matplotlib>=1.3.1->scikit-image)
  Using cached subprocess32-3.2.7.tar.gz
Collecting pytz (from matplotlib>=1.3.1->scikit-image)
  Using cached pytz-2018.3-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib>=1.3.1->scikit-image)
  Using cached backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./lib/Python/lib/python2.7/site-packages (from matplotlib>=1.3.1->scikit-image)
Requirement already satisfied: numpy>=1.7.1 in ./lib/Python/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg (from matplotlib>=1.3.1->scikit-image)
Collecting kiwisolver>=1.0.1 (from matplotlib>=1.3.1->scikit-image)
  Using cached kiwisolver-1.0.1-cp27-cp27m-manylinux1_x86_64.whl
Collecting decorator>=4.1.0 (from networkx>=1.8->scikit-image)
  Using cached decorator-4.2.1-py2.py3-none-any.whl
Requirement already satisfied: setuptools in ./lib/Python/lib/python2.7/site-packages/setuptools-36.6.0.post20171220-py2.7.egg (from kiwisolver>=1.0.1->matplotlib>=1.3.1->scikit-image)
Building wheels for collected packages: networkx, subprocess32
  Running setup.py bdist_wheel for networkx: started
  Running setup.py bdist_wheel for networkx: finished with status 'error'
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-yeDhnL/networkx/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" bdist_wheel -d /tmp/tmpon3uEHpip-wheel- --python-tag cp27:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed building wheel for networkx
  Running setup.py clean for networkx
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-yeDhnL/networkx/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" clean --all:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed cleaning build dir for networkx
  Running setup.py bdist_wheel for subprocess32: started
  Running setup.py bdist_wheel for subprocess32: finished with status 'error'
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-yeDhnL/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" bdist_wheel -d /tmp/tmpfOfMjBpip-wheel- --python-tag cp27:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed building wheel for subprocess32
  Running setup.py clean for subprocess32
  Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-yeDhnL/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" clean --all:
  usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: --help [cmd1 cmd2 ...]
     or: --help-commands
     or: cmd --help
  
  error: option -u not recognized
  
  ----------------------------------------
  Failed cleaning build dir for subprocess32
Failed to build networkx subprocess32
Installing collected packages: subprocess32, pytz, backports.functools-lru-cache, kiwisolver, matplotlib, decorator, networkx, pillow, PyWavelets, scikit-image
  Running setup.py install for subprocess32: started
    Running setup.py install for subprocess32: finished with status 'error'
    Complete output from command "/home/carrie/Workspace/3D Slicer/Slicer-4.8.1-linux-amd64/bin/SlicerApp-real" -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-yeDhnL/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" install --record /tmp/pip-Kt5oiI-record/install-record.txt --single-version-externally-managed --compile:
    usage: [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: --help [cmd1 cmd2 ...]
       or: --help-commands
       or: cmd --help
    
    error: option -u not recognized

```

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [March 7, 2018, 12:17am UTC](https://discourse.slicer.org/t/error-when-installing-scikit-image-via-python-interactor/2253/2 "2018-03-07T00:17:08Z")

</div>

When there are issues using Slicer application as the _python interpreter_, I suggest to fallback to using a the plain python interpreter also bundled in the Slicer package.

The following could be done:

### Step 1

Open a terminal

### Step 2

Source the Slicer environment

```auto
$ eval $(./Slicer --launcher-show-set-environment-commands)

```

### Step 3

Install the package

_Note that the name of the interpreter bundled with Slicer is `python-real` and not `python`_

```auto
$ python-real -m "pip" install scikit-image
Collecting scikit-image
  Downloading scikit_image-0.13.1-cp27-cp27m-manylinux1_x86_64.whl (35.2MB)
  ...
Collecting matplotlib>=1.3.1 (from scikit-image)
  Downloading matplotlib-2.2.0-cp27-cp27m-manylinux1_x86_64.whl (12.5MB)
  ....
Collecting networkx>=1.8 (from scikit-image)
  Downloading networkx-2.1.zip (1.6MB)

[...]

Building wheels for collected packages: networkx, subprocess32

[...]
Running setup.py bdist_wheel for subprocess32 ... error
  Complete output from command /home/jcfr/Downloads/Slicer-4.8.1-linux-amd64/bin/python-real -u -c "import setuptools, tokenize; __file__ ='/tmp/pip-build-vTIc2o/subprocess32/setup.py';f=getattr(tokenize, 'open', open)( __file__ );code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__ , 'exec'))" bdist_wheel -d /tmp/tmpKY4kdZpip-wheel- --python-tag cp27:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-2.7
  copying subprocess32.py -> build/lib.linux-x86_64-2.7
  running build_ext
  building '_posixsubprocess' extension
  creating build/temp.linux-x86_64-2.7
  /usr/bin/gcc-4.6 -pthread -Wall -Wstrict-prototypes -fno-strict-aliasing -fwrapv -g -fPIC -I/home/jcfr/Downloads/Slicer-4.8.1-linux-amd64/lib/Python/include/python2.7 -c _posixsubprocess.c -o build/temp.linux-x86_64-2.7/_posixsubprocess.o
  unable to execute '/usr/bin/gcc-4.6': No such file or directory
  error: command '/usr/bin/gcc-4.6' failed with exit status 1
  
  ----------------------------------------
  Failed building wheel for subprocess32
  Running setup.py clean for subprocess32

[...]

```

### issue

While there are python 2.7 wheels for most of the dependencies (scikit\_image itself, matplotlib, etc …), there are no per-built binaries for `subprocess32` for linux for python 2.7. See [https://pypi.python.org/pypi/subprocess32/3.5.0rc1](https://pypi.python.org/pypi/subprocess32/3.5.0rc1) and [https://pypi.python.org/pypi/subprocess32/3.2.7](https://pypi.python.org/pypi/subprocess32/3.2.7)

On linux, the expectation is that user of the package is expected to build from source.

Few approaches:

- Fix the build system of [https://github.com/google/python-subprocess32](https://github.com/google/python-subprocess32) so that they use [scikit-build](http://scikit-build.readthedocs.io/en/latest/) to compile their code and generate while for python 2.7.

- Use ITK python. Running `pip install itk` is expected to work. See [http://itkpythonpackage.readthedocs.io/en/latest/](http://itkpythonpackage.readthedocs.io/en/latest/)