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pip install gensim==4.2.0 raises deprecation warning #3414

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labouz opened this issue Dec 14, 2022 · 2 comments
Open

pip install gensim==4.2.0 raises deprecation warning #3414

labouz opened this issue Dec 14, 2022 · 2 comments

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@labouz
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labouz commented Dec 14, 2022

When installing gensim in a fresh environment I get the following warning:
Sorry it is a lot of output. The command is pip3 install gensim--4.2.0
my pip version is 22.3.1 and python version 3.11 (see below)

because of character limits, i have cut out chunks of the output to just the warnings:

      ...
      running egg_info
      writing gensim.egg-info/PKG-INFO
      writing dependency_links to gensim.egg-info/dependency_links.txt
      writing requirements to gensim.egg-info/requires.txt
      writing top-level names to gensim.egg-info/top_level.txt
      reading manifest file 'gensim.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      warning: no files found matching 'COPYING.LESSER'
      warning: no files found matching 'ez_setup.py'
      warning: no files found matching 'gensim/models/doc2vec_inner.c'
      adding license file 'COPYING'
      writing manifest file 'gensim.egg-info/SOURCES.txt'
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.DTM' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.DTM' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.DTM' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.DTM' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.PathLineSentences' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.PathLineSentences' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.PathLineSentences' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.PathLineSentences' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.old_d2v_models' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.old_d2v_models' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.old_d2v_models' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.old_d2v_models' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.old_w2v_models' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.old_w2v_models' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.old_w2v_models' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.old_w2v_models' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      copying gensim/_matutils.c -> build/lib.macosx-10.9-universal2-cpython-311/gensim
      copying gensim/_matutils.pyx -> build/lib.macosx-10.9-universal2-cpython-311/gensim
      ...
      copying gensim/corpora/_mmreader.c -> build/lib.macosx-10.9-universal2-cpython-311/gensim/corpora
      copying gensim/corpora/_mmreader.pyx -> build/lib.macosx-10.9-universal2-cpython-311/gensim/corpora
      running build_ext
      building 'gensim.models.word2vec_inner' extension
      creating build/temp.macosx-10.9-universal2-cpython-311
      creating build/temp.macosx-10.9-universal2-cpython-311/gensim
      creating build/temp.macosx-10.9-universal2-cpython-311/gensim/models
      clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include -c gensim/models/word2vec_inner.c -o build/temp.macosx-10.9-universal2-cpython-311/gensim/models/word2vec_inner.o
      In file included from gensim/models/word2vec_inner.c:706:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated 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 " \
       ^
      gensim/models/word2vec_inner.c:12424:5: error: incomplete definition of type 'struct _frame'
          __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      gensim/models/word2vec_inner.c:457:62: note: expanded from macro '__Pyx_PyFrame_SetLineNumber'
        #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
                                                            ~~~~~~~^
      /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'struct _frame'
      typedef struct _frame PyFrameObject;
                     ^
      1 warning and 1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for gensim
  Running setup.py clean for gensim
Failed to build gensim
Installing collected packages: gensim
  Running setup.py install for gensim ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for gensim did not run successfully.
  │ exit code: 1
  ╰─> [540 lines of output]
      running install
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.9-universal2-cpython-311
      creating build/lib.macosx-10.9-universal2-cpython-311/gensim
      ...
      copying gensim/corpora/svmlightcorpus.py -> build/lib.macosx-10.9-universal2-cpython-311/gensim/corpora
      copying gensim/corpora/hashdictionary.py -> build/lib.macosx-10.9-universal2-cpython-311/gensim/corpora
      running egg_info
      writing gensim.egg-info/PKG-INFO
      writing dependency_links to gensim.egg-info/dependency_links.txt
      writing requirements to gensim.egg-info/requires.txt
      writing top-level names to gensim.egg-info/top_level.txt
      reading manifest file 'gensim.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      warning: no files found matching 'COPYING.LESSER'
      warning: no files found matching 'ez_setup.py'
      warning: no files found matching 'gensim/models/doc2vec_inner.c'
      adding license file 'COPYING'
      writing manifest file 'gensim.egg-info/SOURCES.txt'
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.DTM' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.DTM' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.DTM' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.DTM' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.PathLineSentences' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.PathLineSentences' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.PathLineSentences' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.PathLineSentences' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.old_d2v_models' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.old_d2v_models' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.old_d2v_models' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.old_d2v_models' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'gensim.test.test_data.old_w2v_models' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'gensim.test.test_data.old_w2v_models' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'gensim.test.test_data.old_w2v_models' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'gensim.test.test_data.old_w2v_models' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      copying gensim/_matutils.c -> build/lib.macosx-10.9-universal2-cpython-311/gensim
      copying gensim/_matutils.pyx -> build/lib.macosx-10.9-universal2-cpython-311/gensim
     ...
      copying gensim/corpora/_mmreader.pyx -> build/lib.macosx-10.9-universal2-cpython-311/gensim/corpora
      running build_ext
      building 'gensim.models.word2vec_inner' extension
      creating build/temp.macosx-10.9-universal2-cpython-311
      creating build/temp.macosx-10.9-universal2-cpython-311/gensim
      creating build/temp.macosx-10.9-universal2-cpython-311/gensim/models
      clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include -c gensim/models/word2vec_inner.c -o build/temp.macosx-10.9-universal2-cpython-311/gensim/models/word2vec_inner.o
      In file included from gensim/models/word2vec_inner.c:706:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
      In file included from /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
      /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated 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 " \
       ^
      gensim/models/word2vec_inner.c:12424:5: error: incomplete definition of type 'struct _frame'
          __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      gensim/models/word2vec_inner.c:457:62: note: expanded from macro '__Pyx_PyFrame_SetLineNumber'
        #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
                                                            ~~~~~~~^
      /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'struct _frame'
      typedef struct _frame PyFrameObject;
                     ^
      1 warning and 1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> gensim

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Versions

Please provide the output of:

>>> import platform; print(platform.platform())

import sys; print("Python", sys.version)

import struct; print("Bits", 8 * struct.calcsize("P"))

import numpy; print("NumPy", numpy.__version__)

import scipy; print("SciPy", scipy.__version__)
macOS-12.5-arm64-arm-64bit
>>> 
>>> import sys; print("Python", sys.version)
Python 3.11.1 (v3.11.1:a7a450f84a, Dec  6 2022, 15:24:06) [Clang 13.0.0 (clang-1300.0.29.30)]
>>> 
>>> import struct; print("Bits", 8 * struct.calcsize("P"))
Bits 64
>>> 
>>> import numpy; print("NumPy", numpy.__version__)
NumPy 1.23.5
>>> 
>>> import scipy; print("SciPy", scipy.__version__)
SciPy 1.9.3
@mpenkov
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mpenkov commented Dec 15, 2022 •
edited by piskvorky

Can you try updating setup.py and see if this fixes the problem?

I think the relevant part is the find_packages call on line 354. If you change that to find_namespace_packages (excluding the test data explicitly), does the warning go away?

Also, 4.2.0 won't build under Py3.11, please use the develop HEAD branch.

@labouz
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labouz commented Dec 15, 2022

thank you! i was able to get gensim running by installing the develop branch. i have not yet tried modifying setup.py, will try that and see

@bdpedigo bdpedigo mentioned this issue Jan 3, 2023
Closed
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@mpenkov @labouz