[mlpack] issue with mlpack Python bindings on Mac OsX

[Frodo Jedi]

Hi Ryan,
thanks again ;-)
So yes, if I type import mplack this time there is no error.

As per your requests, this is the output of cmake ... from a new clean
build directory


-- The C compiler identification is AppleClang 9.0.0.9000039
-- The CXX compiler identification is AppleClang 9.0.0.9000039
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- cotire 1.7.10 loaded.
-- Found Armadillo: /usr/local/lib/libarmadillo.dylib (found suitable
version "9.100.5", minimum required is "6.500.0")
-- Armadillo libraries: /usr/local/lib/libarmadillo.dylib
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   program_options
--   unit_test_framework
--   serialization
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS
OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Found Git: /usr/local/bin/git (found version "2.19.0")
-- Regenerating arma_config.hpp.
CMake Warning at CMakeLists.txt:425 (message):
  txt2man not found; man pages will not be generated.


-- Found PythonInterp: /usr/local/bin/python (found version "2.7.15")
-- Found Python: /usr/local/bin/python
-- Found PY_distutils: /usr/local/Cellar/python at 2
/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils
-- Found PY_Cython: /usr/local/lib/python2.7/site-packages/Cython
-- Found PY_numpy: /usr/local/lib/python2.7/site-packages/numpy
-- Found PY_pandas: /usr/local/lib/python2.7/site-packages/pandas
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- CXX target mlpack cotired.
-- CXX target mlpack_test cotired.
-- Found Doxygen: /usr/local/bin/doxygen (found version "1.8.14") found
components:  doxygen missing components:  dot
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Configuring done
-- Generating done
-- Build files have been written to:
/Users/frodo/Documents/Machine_learning/mlpack-3.0.4/build


Then I run make -j4 (as normal user, not with sudo) and then I run sudo
make install. No error was detected so I guess now everything should work.

I was wondering, how can I fully check that everything is solved and works
at 100%? Any further test?


Cheers


FJ








On Thu, Dec 27, 2018 at 11:25 PM Ryan Curtin <ryan at ratml.org> wrote:

> On Thu, Dec 27, 2018 at 08:23:33PM +0100, Frodo Jedi wrote:
> > Hi Ryan,
> > thanks.
> >
> > This is the output of cmake .. from a empty build directory:
>
> Perfect... I think this isolates what the problem is:
>
> > -- We will call setup.py install with --prefix=/usr/local --root=
>
> It's a bit strange to call --root= with no option, so I thought this was
> the problem.  And then someone else opened an issue on Github with the
> same problem, but they were running Linux:
>
> https://github.com/mlpack/mlpack/issues/1621
>
> At this point I realized I could reproduce the issue.  The solution,
> then, was to make sure we were calling --root="" when $ENV{DESTDIR} was
> empty.
>
> So here is another patched CMakeLists.txt; can you drop it in place,
> remove the build directory you were using, and try again?  I think that
> this should work...
>
> http://www.ratml.org/misc/CMakeLists.mod2.txt
>
> If it does, I'll open a PR and we'll get the change merged in so it
> doesn't happen again.
>
> One other note is, looking at the output you gave, it appears that
> mlpack did successfully install, so if you run Python, 'import mlpack'
> should work:
>
> > Extracting mlpack-3.0.4-py2.7-macosx-10.12-x86_64.egg to
> /usr/local/lib/python2.7/site-packages
> > Adding mlpack 3.0.4 to easy-install.pth file
> > Installed
> /usr/local/lib/python2.7/site-packages/mlpack-3.0.4-py2.7-macosx-10.12-x86_64.egg
>
> Thanks for the detailed output in this process; that was integral to
> getting it figured out (assuming that we got it this time :)).
>
> Ryan
>
> --
> Ryan Curtin    | "That rug really tied the room together."
> ryan at ratml.org |   - The Dude
>
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