Install error

[dkirkby]

I am trying to install using:

git clone --recurse-submodules [email protected]:jmeyers314/batoid.git
cd batoid
python setup.py install

My build log is attached: install.log

[jmeyers314]

Weird. The best my google-fu can come up with so far is maybe something compiler related? (What compiler are you using?)

Do you know if you can compile something simple with #include <algorithm> in it?

Actually, I think that version of table.h, which I modified from GalSim's version, may not even depend on anymore, so you could also try removing that line.

[dkirkby]

It looks like I am picking up c++ from my conda env (which surprised me):

(raytrace) batoid% which c++
/Users/david/anaconda3/envs/raytrace/bin/c++

Also, my cmake (which I hardly ever use) is probably quite old:

% cmake --version
cmake version 3.5.2

[dkirkby]

I just checked that my other conda envs do not shadow c++, so perhaps this is a recent feature? (I just created this env today). This is the conda version of c++:

(raytrace) batoid% c++ --version
c++ (GCC) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

There are some notes here about the interaction of cmake with the conda compilers that might be relevant.

[dkirkby]

I tried again with a different conda env:

conda create -n raytrace python=3.7 pip ipython jupyter jupyterlab ipykernel numpy scipy pandas matplotlib
conda activate raytrace
git clone --recurse-submodules [email protected]:jmeyers314/batoid.git
cd batoid
python setup.py install

This time it worked.

Looking back at my previous attempt, I realized that I included gcc in my conda env (blindly cutting & pasting from another project), so perhaps there is still an issue that batoid does not install with gcc 4.8.5 and/or the conda compilers.

[jmeyers314]

Thanks David, I'll try looking into using anaconda compilers. Glad you found a way around this in the meantime.

FWIW, this page indicates that __has_include isn't available in gcc until version 5. I guess the problematic bit is that the anaconda compiler ultimately included system files from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/
instead of just staying within its own version of the standard library.