Cython installation fails with pip - Cython.Runtime.refnanny extension

I’m not sure whether this is a Cython or a pip issue, but building Cython using pip install --upgrade cython failed for me on two quite different python-2.7 installations during the step of building the Cython.Runtime.refnanny extension. One machine was Mac OS X Sierra with python installed from homebrew and using virtualenv. The other machine was on our linux cluster running CentOs. Virtualenv was present in both cases.

bash-4.1$ pip install --upgrade cython
Downloading/unpacking cython
  Downloading Cython-0.25.tar.gz (1.7Mb): 1.7Mb downloaded
  Running setup.py egg_info for package cython
    Unable to find pgen, not compiling formal grammar.

 .... skipping lots ...


    gcc -pthread -shared build/temp.linux-x86_64-2.7/home/xxx/virtualenvs/volker-py27/build/cython/Cython/Compiler/Code.o -L/g/software/linux/pack/python-2.7/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/Cython/Compiler/Code.so
    building 'Cython.Runtime.refnanny' extension
    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/g/software/linux/pack/python-2.7/include/python2.7 -c /home/xxx/virtualenvs/volker-py27/build/cython/Cython/Runtime/refnanny.c -o build/temp.linux-x86_64-2.7/home/xxx/virtualenvs/volker-py27/build/cython/Cython/Runtime/refnanny.o
    gcc: /home/xxx/virtualenvs/volker-py27/build/cython/Cython/Runtime/refnanny.c: No such file or directory 

pathnames above slightly anonymized

[robertwb]

I think I figured this out. It was due to a really old version of setuptools being used.

[totaam]

yum install python-devel gcc IIRC, that’s all I needed on centos 6.x to build Cython.