pip install centrosome tries compiling *.c

[LeeKamentsky]

From Christian Tischner:
(pip install centrosome)

now i did it again with the --system-site-packages and it ran quite far....till i got below error. I ran pip being inside the virtualenv...do i maybe have to explicitly tell it that it should install everything into the virtualenv and not globally?!

building '*' extension

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/g/software/linux/pack/python-2.7/lib/python2.7/site-packages/numpy/core/include -Icentrosome/include -I/g/software/linux/pack/python-2.7/include/python2.7 -c centrosome/.c -o build/temp.linux-x86_64-2.7/centrosome/.o

gcc: centrosome/*.c: No such file or directory

gcc: no input files

error: command 'gcc' failed with exit status 1

[LeeKamentsky]

I think the culprit is here:
https://github.com/CellProfiler/centrosome/blob/master/setup.py#L82
I will fix.

[LeeKamentsky]

I tried "pip install centrosome" on our Centos 6.5 / Python 2.7 here and it worked. I am guessing that there is a difference in the way setuptools parses the cython extension commands between mine and yours.

Can you do:

pip freeze
python -c "import setuptools;print setuptools.version"

[LeeKamentsky]

You can try out my fix like this:

pip install https://github.com/CellProfiler/centrosome/archive/issues/48.tar.gz#egg=centrosome

[tischi]

my pip version is 7.1.2
my setuptools version is 0.6.c11

pip install https://github.com/CellProfiler/centrosome/archive/issues/48.tar.gz#egg=centrosome

gave the following, different error:

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/g/software/linux/pack/python-2.7/lib/python2.7/site-packages/numpy/core/include -Icentrosome/include -I/g/software/linux/pack/python-2.7/include/python2.7 -c centrosome/src/_cpmorphology.c -o build/temp.linux-x86_64-2.7/centrosome/src/_cpmorphology.o
In file included from /g/software/linux/pack/python-2.7/include/python2.7/Python.h:8,
                 from centrosome/src/_cpmorphology.c:24:
/g/software/linux/pack/python-2.7/include/python2.7/pyconfig.h:1149:1: warning: "_POSIX_C_SOURCE" redefined
In file included from /usr/include/stdlib.h:25,
                 from centrosome/src/_cpmorphology.c:22:
/usr/include/features.h:213:1: warning: this is the location of the previous definition
centrosome/src/_cpmorphology.c:27: warning: ‘to_stdout’ defined but not used
gcc -pthread -shared build/temp.linux-x86_64-2.7/centrosome/src/_cpmorphology.o -L/g/software/linux/pack/python-2.7/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/_cpmorphology.so
building '_convex_hull' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/g/software/linux/pack/python-2.7/lib/python2.7/site-packages/numpy/core/include -Icentrosome/include -I/g/software/linux/pack/python-2.7/include/python2.7 -c centrosome/_convex_hull.c -o build/temp.linux-x86_64-2.7/centrosome/_convex_hull.o
gcc: centrosome/_convex_hull.c: No such file or directory
gcc: no input files
error: command 'gcc' failed with exit status 1

[tischi]

after attempting to install centrosome i ran

pip freeze

cycler==0.9.0
Cython==0.14.1
decorator==4.0.5
docutils==0.7
fpconst==0.7.2
h5py==1.3.1
hcluster==0.2.0
Jinja2==2.5.5
LIBSVM==2.89
matplotlib==1.5.0
mpi4py==1.2.2
MySQL-python==1.2.3
netCDF4==0.9.1
networkx==1.10
nose==1.0.0
numpy==1.6.0
PIL==1.1.7
Pillow==3.0.0
PyAMF==0.6.1
pyarmor==2.5.2
Pygments==1.4
pyparsing==2.0.6
python-dateutil==2.4.2
pytz==2015.7
PyYAML==3.10
rpy2==2.2.6.dev20120914
scikit-image==0.11.3
scikit-learn==0.9
scipy==0.9.0
six==1.10.0
SOAPpy==0.12.5
Sphinx==1.0.7
SQLAlchemy==0.7.5
virtualenv==1.7
wstools==0.3

[LeeKamentsky]

@tischi your setuptools is ancient - from 2009. Cython is pretty old too. I would upgrade both inside your virtualenv. The directions for setuptools are here: https://pypi.python.org/pypi/setuptools

wget https://bootstrap.pypa.io/ez_setup.py -O - | python

Cython can be upgraded like this:

pip install --upgrade --no-deps Cython

I think you should be good after that.

[tischi]

now it worked!

Successfully installed centrosome-1.0.3

however, i had to slightly change the upgrade of setuptools:

update setuptools

wget --no-check-certificate https://bootstrap.pypa.io/ez_setup.py
python ez_setup.py --insecure

[ssyip]

Hi,

I am trying to install centrosome on window with python 3.6. , but got the following error (attached) from "pip install centrosome". Does anyone know how to fix it? Thank you so much!