Carsten Haubold

`CFLAGS` was set in the bash_profile of the Mac that we encountered the error on. So, I guess that checking and warning the user should be sufficient. But I am...

All right, agree!

Oh right, good catch, this is a relict. I'll remove the reference to the patch as we updated pgmlink's CMakeLists.txt.

Regarding https://github.com/janelia-flyem/buildem/commit/190ac3f, you added this flag right around the time when I first tried to build on Mac using GCC, and so I relied on this way to pass the...

@JensNRAD: for OpenGM the change is to set `-DPYTHON_NUMPY_INCLUDE_DIR` to the path mentioned above, not `-DPYTHON_INCLUDE_DIR`, right?

Your settings probably work as well because there is this second PYTHON_INCLUDE_DIR. I think this is the supposed configuration: ``` PYTHON_EXECUTABLE /home/chaubold/ilastik-buildem/bin/python PYTHON_INCLUDE_DIR /home/chaubold/ilastik-buildem/include/python2.7 PYTHON_INCLUDE_DIR2 /home/chaubold/ilastik-buildem/include/python2.7 PYTHON_LIBRARY /home/chaubold/ilastik-buildem/lib/libpython2.7.so PYTHON_LIBRARY_DEBUG PYTHON_LIBRARY_DEBUG-NOTFOUND...

When merging John's branch, a new version of h5py is installed which brings new modules. To build an OSX binary with that, in the `setup_mac.py` file of ilastik we also...

> So, which gcc and g++ are they referring too then? We are building everyting with GCC 4.8 (installed via Homebrew or Mac Ports), as we need the CPLEX Optimizer,...

@stuarteberg, we have look into this again next week, as buildem's master branch still does not build ilastik's conservation tracking dependencies...

> Started pixel classification in three dimensions and exported it to (z,y,x) .h5 (this allowed me to open the prediction in matlab with the native dimensions of the raw data...