conda-recipe: On OSX, the binary includes an extraneous LC_RPATH command

[stuarteberg]

(I'm just opening this issue here so I don't forget about it. You can probably stop reading.)

For some reason, the _nifty.so file produced by the conda recipe has an extra LC_RPATH that doesn't get properly cleaned up in the conda post-processing step. You can see it by inspecting the output of otool -l:

$ otool -l /miniconda2/envs/ilastik-new/lib/python2.7/site-packages/nifty/_nifty.so | grep -A 2 -B 1 LC_RPATH
Load command 17
          cmd LC_RPATH
      cmdsize 40
         path /miniconda2/envs/_build/lib (offset 12)
--
--
Load command 20
          cmd LC_RPATH
      cmdsize 40
         path @loader_path/../../../ (offset 12)

The second LC_RPATH entry is correct, but the first one (/miniconda2/envs/_build/lib) shouldn't be there. It references the _build environment on my machine. For most people, this will not cause any problems whatsoever. But if that directory happens to exist on your machine, then you'll get an error when you try to use nifty:

Fatal Python error: PyThreadState_Get: no current thread

That's because it's loading the wrong libpython2.7.dylib at runtime.

PS -- Note for mac users (okay, just me): diagnosing this issue was made easier with the DYLD_PRINT_RPATHS environment variable.

[DerThorsten]

Hi @stuarteberg,

I swichted to a new version of pybind11 which defines a cmake-function to add python modules.
This could change a lot (also this might undo some fixes...)

[stuarteberg]

OK, thanks for the warning.