[Bug report] Installation Fails: python do.py run-python

[blankjul]

python do.py run-python does not run successfully.
The rights should be fine and even sudo did not help.

Any easy fix for this?

• Operating system: Mac 12.0.1
• COCO version: Github Version
• Apple clang version 13.0.0 (clang-1300.0.29.3)

(I have experimented with to modifying coco.h and interface.pyx but was not successful)

/----------------------------< EXCEPTION MESSAGE >----------------------------\
|                                                                             |
| NOTE: Using precompiled C file to build interface.                          |
| running install                                                             |
| running bdist_egg                                                           |
| running egg_info                                                            |
| creating cocoex.egg-info                                                    |
| writing cocoex.egg-info/PKG-INFO                                            |
| writing dependency_links to cocoex.egg-info/dependency_links.txt            |
| writing top-level names to cocoex.egg-info/top_level.txt                    |
| writing manifest file 'cocoex.egg-info/SOURCES.txt'                         |
| reading manifest file 'cocoex.egg-info/SOURCES.txt'                         |
| reading manifest template 'MANIFEST.in'                                     |
| adding license file 'LICENSE'                                               |
| adding license file 'AUTHORS'                                               |
| writing manifest file 'cocoex.egg-info/SOURCES.txt'                         |
| installing library code to build/bdist.macosx-10.9-x86_64/egg               |
| running install_lib                                                         |
| running build_py                                                            |
| creating build                                                              |
| creating build/lib.macosx-10.9-x86_64-3.8                                   |
| creating build/lib.macosx-10.9-x86_64-3.8/cocoex                            |
| copying python/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/cocoex       |
| copying python/solvers.py -> build/lib.macosx-10.9-x86_64-3.8/cocoex        |
| copying python/exceptions.py -> build/lib.macosx-10.9-x86_64-3.8/cocoex     |
| copying python/utilities.py -> build/lib.macosx-10.9-x86_64-3.8/cocoex      |
| running build_ext                                                           |
| building 'cocoex.interface' extension                                       |
| creating build/temp.macosx-10.9-x86_64-3.8                                  |
| creating build/temp.macosx-10.9-x86_64-3.8/cython                           |
| gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrap |
| v -O3 -Wall -Wstrict-prototypes -I/Users/blankjul/anaconda3/anaconda3/envs/ |
| dev/include -arch x86_64 -I/Users/blankjul/anaconda3/anaconda3/envs/dev/inc |
| lude -arch x86_64 -I/Users/blankjul/anaconda3/anaconda3/envs/dev/lib/python |
| 3.8/site-packages/numpy/core/include -I/Users/blankjul/anaconda3/anaconda3/ |
| envs/dev/include/python3.8 -c cython/interface.c -o build/temp.macosx-10.9- |
| x86_64-3.8/cython/interface.o                                               |
| In file included from cython/interface.c:593:                               |
| In file included from /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/pyth |
| on3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:               |
| In file included from /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/pyth |
| on3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:            |
| In file included from /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/pyth |
| on3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:           |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/python3.8/site-packages/nu |
| mpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using depre |
| cated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API  |
| NPY_1_7_API_VERSION" [-W#warnings]                                          |
| #warning "Using deprecated NumPy API, disable it with " \                   |
|  ^                                                                          |
| cython/interface.c:12008:7: error: implicit declaration of function 'bbob_b |
| iobj_problem_best_parameter_print' is invalid in C99 [-Werror,-Wimplicit-fu |
| nction-declaration]                                                         |
|       bbob_biobj_problem_best_parameter_print(__pyx_v_self->problem);       |
|       ^                                                                     |
| cython/interface.c:12028:7: error: implicit declaration of function 'bbob_p |
| roblem_best_parameter_print' is invalid in C99 [-Werror,-Wimplicit-function |
| -declaration]                                                               |
|       bbob_problem_best_parameter_print(__pyx_v_self->problem);             |
|       ^                                                                     |
| cython/interface.c:18650:39: warning: 'tp_print' is deprecated [-Wdeprecate |
| d-declarations]                                                             |
|   __pyx_type_6cocoex_9interface_Suite.tp_print = 0;                         |
|                                       ^                                     |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/cpython/obje |
| ct.h:260:5: note: 'tp_print' has been explicitly marked deprecated here     |
|     Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);            |
|     ^                                                                       |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/pyport.h:515 |
| :54: note: expanded from macro 'Py_DEPRECATED'                              |
| #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))       |
|                                                      ^                      |
| cython/interface.c:18679:42: warning: 'tp_print' is deprecated [-Wdeprecate |
| d-declarations]                                                             |
|   __pyx_type_6cocoex_9interface_Observer.tp_print = 0;                      |
|                                          ^                                  |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/cpython/obje |
| ct.h:260:5: note: 'tp_print' has been explicitly marked deprecated here     |
|     Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);            |
|     ^                                                                       |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/pyport.h:515 |
| :54: note: expanded from macro 'Py_DEPRECATED'                              |
| #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))       |
|                                                      ^                      |
| cython/interface.c:18689:41: warning: 'tp_print' is deprecated [-Wdeprecate |
| d-declarations]                                                             |
|   __pyx_type_6cocoex_9interface_Problem.tp_print = 0;                       |
|                                         ^                                   |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/cpython/obje |
| ct.h:260:5: note: 'tp_print' has been explicitly marked deprecated here     |
|     Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);            |
|     ^                                                                       |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/pyport.h:515 |
| :54: note: expanded from macro 'Py_DEPRECATED'                              |
| #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))       |
|                                                      ^                      |
| cython/interface.c:18708:62: warning: 'tp_print' is deprecated [-Wdeprecate |
| d-declarations]                                                             |
|   __pyx_type_6cocoex_9interface___pyx_scope_struct____iter__.tp_print = 0;  |
|                                                              ^              |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/cpython/obje |
| ct.h:260:5: note: 'tp_print' has been explicitly marked deprecated here     |
|     Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);            |
|     ^                                                                       |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/include/python3.8/pyport.h:515 |
| :54: note: expanded from macro 'Py_DEPRECATED'                              |
| #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))       |
|                                                      ^                      |
| 5 warnings and 2 errors generated.                                          |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/python3.8/site-packages/se |
| tuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py inst |
| all is deprecated. Use build and pip and other standards-based tools.       |
|   warnings.warn(                                                            |
| /Users/blankjul/anaconda3/anaconda3/envs/dev/lib/python3.8/site-packages/se |
| tuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_i |
| nstall command is deprecated. Use build and pip and other standards-based t |
| ools.                                                                       |
|   warnings.warn(                                                            |
| error: command 'gcc' failed with exit status 1                              |

[ttusar]

Thanks for the report. We are aware of the issue (#2028), but have yet to publish a fix. In the meantime, you can work around it by making some non-consequential change to the file code-experiments/build/python/cython/interface.pyx (such as adding a space or comment) and rerunning the command. This should trigger cython compilation (instead of using precompiled files) and the error should disappear.

In case that doesn’t work, remove lines 770-775 of the file code-experiments/build/python/cython/interface.pyx.

Let us know how it goes.

[blankjul]

Rerunning cython did not do the job. I have tried this before and even added the method declaration to the file.

Commenting out the lines - as you have suggested - worked! Thanks for your quick help!