Building graph-tool on OSX with Python 3.4

Question

I tried to install graph-tool on Mac OSX 10.10 using homebrew. The brew build process works fine, but when I try to import graph-tool I get the error described in this question . Another problem with homebrew is that I always builds graph-tool for python2.7 and it installs the packages in the Python 2.7 sit-packages folder. But I want to use it with Python 3.4. These are the reasons why I tried to build graph-tool from source.

The ./configure command automatically uses Python 2.7, too. So I passed it the desired Python version with ./configure PYTHON=python3.4

It then detects the correct version as well as the related paths but crash with the following error:

configure: error:
Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"

====================================================================== ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them.

======================================================================

The error occurs with and without PYTHON variable set. From the output of ./configure I can see that everything works fine except for the last line, which says:

checking consistency of all components of python development environment... no

Whats does the above line mean and how do I properly install graph-tool on my maschine?

Answer 1

The error message is explaining exactly what needs to be done. Since python was installed in a non-standard path, you need to pass the flag LDFLAGS="-L/usr/non-standard-path/python/lib" pointing to the directory where the python libraries are located. This is most likely "/usr/local/lib" , if you are using homebrew.

Answer 2

I was getting this error when I was trying to install graph-tool using outdated an autoconf / automake / pkg-config combination (installed using yum in CentOS 5.10). Installing those packages from source fixed the problem... although I'm not sure how this related to my python installation....

Answer 3

It worked for me by passing the variable PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -F/usr/local/Cellar/python3/3.6.3/Frameworks -framework CoreFoundation" .
In your case, it would be the path to the homebrew installation of python3.4 .
The way I found out is that in the config.log , the error message shows the following:

configure:19023: checking python extra libraries
configure:19030: result: -ldl  -framework CoreFoundation 
configure:19037: checking python extra linking flags
configure:19044: result: -Wl,-stack_size,1000000  -framework CoreFoundation Python.framework/Versions/3.6/Python
configure:19051: checking consistency of all components of python development environment
configure:19079: gcc -o conftest -g -O2 -DNDEBUG  -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m -F/usr/local/Cellar/python3/3.6.3/Frameworks/ -Wl,-stack_size,1000000  -framework CoreFoundation Python.framework/Versions/3.6/Python conftest.c  -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6m -ldl  -framework CoreFoundation  -ldl  -framework CoreFoundation  >&5
clang: error: no such file or directory: 'Python.framework/Versions/3.6/Python'

The error seems to be path 'Python.framework/Versions/3.6/Python' , that in a homebrew installation does not exist. I search for the same path in the config.log and I found this line:

PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python"

So, the solution for me was to pass this variable with the right path.