build scipy error cythonize failed

Question

I'm trying to build scipy and I get a RuntimeError:

$sudo python setup.py build
Processing scipy/cluster/_vq_rewrite.pyx
Traceback (most recent call last):
  File "tools/cythonize.py", line 172, in <module>
    main()
  File "tools/cythonize.py", line 168, in main
    find_process_files(root_dir)
  File "tools/cythonize.py", line 160, in find_process_files
    process(cur_dir, fromfile, tofile, function, hash_db)
  File "tools/cythonize.py", line 137, in process
    processor_function(fromfile, tofile)
  File "tools/cythonize.py", line 66, in process_pyx
    raise OSError('Cython needs to be installed')
OSError: Cython needs to be installed

Traceback (most recent call last):
  File "setup.py", line 209, in <module>
    setup_package()
  File "setup.py", line 202, in setup_package
    generate_cython()
  File "setup.py", line 147, in generate_cython
    raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!

What are the ways to provide cython to remedy this error?

score 87 · Answer 1 · edited May 13 '15 at 15:58

87

Python setuptools solved the problem.

http://docs.cython.org/src/quickstart/install.html
easy_install cython or pip install cython

edited May 13 '15 at 15:58

Roman

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answered Mar 02 '13 at 16:03

Liatz

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25

Wouldn't it be nice to include that in the documentation of scipy? – W7GVR Jul 11 '15 at 19:35
1

or as an automatic dependency? – reticivis Dec 14 '21 at 20:40

score 3 · Answer 2 · answered May 24 '19 at 14:21

3

If you do not have Cython installed then use: pip install Cython. However, if you do have an old version of Cython installed like me then this is what solved it for me: pip install --upgrade Cython

answered May 24 '19 at 14:21

SuperKogito

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score 0 · Answer 3 · answered Nov 02 '22 at 03:09

0

For me, this problem occurred due to incompatible python + pandas versions due to incorrect environment configurations despite using Anaconda. Installing Cython via pip worked too, but that wasn't the real solution.

answered Nov 02 '22 at 03:09

Akash Agarwal

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score 0 · Answer 4 · answered Jun 22 '23 at 09:07

0

I installed Cython which did not solve the problem. I solved it by upgrading my pip: pip3 install --upgrade pip.

answered Jun 22 '23 at 09:07

tschomacker

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build scipy error cythonize failed

4 Answers4

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