Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[BUG] Installing giotto-tda error #674

Closed
mubagriyanik opened this issue Jul 11, 2023 · 6 comments
Closed

[BUG] Installing giotto-tda error #674

mubagriyanik opened this issue Jul 11, 2023 · 6 comments
Labels
bug Something isn't working

Comments

@mubagriyanik
Copy link

mubagriyanik commented Jul 11, 2023 •
edited

Hello,

I am trying to install giotto tda by using this code provided on the website:

pip install giotto-tda

I use comda environment and when I ran this code on the conda environment this is the code line and error I am getting:

`
Building wheels for collected packages: giotto-tda
Building wheel for giotto-tda (setup.py) ... /Password:
error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [239 lines of output]
/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options

    opt = self.warn_dash_deprecation(opt, section)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-11.0-arm64-cpython-311
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda
  copying gtda/_version.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda
  copying gtda/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda
  copying gtda/pipeline.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda
  copying gtda/base.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/_metrics.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/features.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/distance.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/preprocessing.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  copying gtda/diagrams/_utils.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/externals
  copying gtda/externals/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/tests
  copying gtda/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/tests
  copying gtda/tests/test_pipeline.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/cover.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/visualization.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/nerve.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/cluster.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/pipeline.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  copying gtda/mapper/filter.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/utils
  copying gtda/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils
  copying gtda/utils/_docs.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils
  copying gtda/utils/testing.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils
  copying gtda/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/embedding.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/features.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/preprocessing.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/multivariate.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  copying gtda/time_series/target.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers
  copying gtda/meta_transformers/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers
  copying gtda/meta_transformers/features.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs
  copying gtda/graphs/geodesic_distance.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs
  copying gtda/graphs/transition.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs
  copying gtda/graphs/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs
  copying gtda/graphs/kneighbors.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/homology
  copying gtda/homology/point_clouds.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology
  copying gtda/homology/consistent.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology
  copying gtda/homology/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology
  copying gtda/homology/_utils.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_features.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_distance.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams/tests
  copying gtda/diagrams/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_preprocessing.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/diagrams/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/cubical_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/simplex_tree_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/strong_witness_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/periodic_cubical_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/witness_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/rips_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/ripser_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  copying gtda/externals/python/cech_complex_interface.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  copying gtda/externals/python/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_witness.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_rips_complex.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_cech_complex.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_periodic_cubical_complex.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/externals/python/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/_logging.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/_cover.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/visualization.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/_cluster.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/pipeline.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/_list_feature_union.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  copying gtda/mapper/utils/decorators.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/mapper/utils
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/utils/tests
  copying gtda/utils/tests/test_validation.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils/tests
  copying gtda/utils/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/utils/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series/tests
  copying gtda/time_series/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series/tests
  copying gtda/time_series/tests/test_multivariate.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series/tests
  copying gtda/time_series/tests/test_embedding.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series/tests
  copying gtda/time_series/tests/test_preprocessing.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/time_series/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/test_features.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/meta_transformers/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs/tests
  copying gtda/graphs/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs/tests
  copying gtda/graphs/tests/test_transition.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs/tests
  copying gtda/graphs/tests/test_geodesic_distance.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs/tests
  copying gtda/graphs/tests/test_kneighbors.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/graphs/tests
  creating build/lib.macosx-11.0-arm64-cpython-311/gtda/homology/tests
  copying gtda/homology/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology/tests
  copying gtda/homology/tests/test_consistent.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology/tests
  copying gtda/homology/tests/test_point_clouds.py -> build/lib.macosx-11.0-arm64-cpython-311/gtda/homology/tests
  running build_ext
  Cloning into '/private/var/folders/lq/dh7kcps136n72nc_dhrly7nw0000gn/T/pip-install-wli41gqr/giotto-tda_6d92762b595147ea966f0f4868362d77/gtda/externals/pybind11'...
  -- The CXX compiler identification is Clang 16.0.0
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /Users/mbagriyanik/mambaforge/envs/ufl23/bin/arm64-apple-darwin20.0.0-clang++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- pybind11 v2.11.0 dev1
  -- CMake 3.26.1
  -- Found PythonInterp: /Users/mbagriyanik/mambaforge/envs/ufl23/bin/python (found suitable version "3.11.2", minimum required is "3.6")
  -- Found PythonLibs: /Users/mbagriyanik/mambaforge/envs/ufl23/lib/libpython3.11.dylib
  -- PYTHON 3.11.2
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- pybind11::lto enabled
  -- Performing Test HAS_FLTO_THIN
  -- Performing Test HAS_FLTO_THIN - Success
  -- pybind11::thin_lto enabled
  -- Configuring done (0.5s)
  -- Generating done (0.0s)
  -- Build files have been written to: /private/var/folders/lq/dh7kcps136n72nc_dhrly7nw0000gn/T/pip-install-wli41gqr/giotto-tda_6d92762b595147ea966f0f4868362d77/gtda/externals/pybind11/build
  Install the project...
  -- Install configuration: ""
  -- Up-to-date: /usr/local/include/pybind11
  CMake Error at cmake_install.cmake:41 (file):
    file INSTALL cannot set permissions on "/usr/local/include/pybind11":
    Operation not permitted.
  
  
  make: *** [Makefile:100: install] Error 1
  Install the project...
  -- Install configuration: ""
  -- Up-to-date: /usr/local/include/pybind11
  -- Installing: /usr/local/include/pybind11/attr.h
  -- Installing: /usr/local/include/pybind11/embed.h
  -- Installing: /usr/local/include/pybind11/numpy.h
  -- Installing: /usr/local/include/pybind11/pybind11.h
  -- Installing: /usr/local/include/pybind11/operators.h
  -- Installing: /usr/local/include/pybind11/iostream.h
  -- Installing: /usr/local/include/pybind11/gil.h
  -- Installing: /usr/local/include/pybind11/chrono.h
  -- Installing: /usr/local/include/pybind11/stl_bind.h
  -- Installing: /usr/local/include/pybind11/buffer_info.h
  -- Installing: /usr/local/include/pybind11/options.h
  -- Up-to-date: /usr/local/include/pybind11/eigen
  -- Installing: /usr/local/include/pybind11/eigen/matrix.h
  -- Installing: /usr/local/include/pybind11/eigen/common.h
  -- Installing: /usr/local/include/pybind11/eigen/tensor.h
  -- Up-to-date: /usr/local/include/pybind11/stl
  -- Installing: /usr/local/include/pybind11/stl/filesystem.h
  -- Installing: /usr/local/include/pybind11/functional.h
  -- Installing: /usr/local/include/pybind11/stl.h
  -- Up-to-date: /usr/local/include/pybind11/detail
  -- Installing: /usr/local/include/pybind11/detail/type_caster_base.h
  -- Installing: /usr/local/include/pybind11/detail/typeid.h
  -- Installing: /usr/local/include/pybind11/detail/descr.h
  -- Installing: /usr/local/include/pybind11/detail/internals.h
  -- Installing: /usr/local/include/pybind11/detail/common.h
  -- Installing: /usr/local/include/pybind11/detail/class.h
  -- Installing: /usr/local/include/pybind11/detail/init.h
  -- Installing: /usr/local/include/pybind11/common.h
  -- Installing: /usr/local/include/pybind11/eval.h
  -- Installing: /usr/local/include/pybind11/cast.h
  -- Installing: /usr/local/include/pybind11/type_caster_pyobject_ptr.h
  -- Installing: /usr/local/include/pybind11/eigen.h
  -- Installing: /usr/local/include/pybind11/pytypes.h
  -- Installing: /usr/local/include/pybind11/complex.h
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Config.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11ConfigVersion.cmake
  -- Installing: /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Common.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Tools.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11NewTools.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Targets.cmake
  -- Installing: /usr/local/share/pkgconfig/pybind11.pc
  fatal: not a git repository (or any of the parent directories): .git
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/lq/dh7kcps136n72nc_dhrly7nw0000gn/T/pip-install-wli41gqr/giotto-tda_6d92762b595147ea966f0f4868362d77/setup.py", line 183, in <module>
      setup(name=DISTNAME,
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 343, in run
      self.run_command("build")
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run
      self.run_command(cmd_name)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/private/var/folders/lq/dh7kcps136n72nc_dhrly7nw0000gn/T/pip-install-wli41gqr/giotto-tda_6d92762b595147ea966f0f4868362d77/setup.py", line 116, in run
      self.install_dependencies()
    File "/private/var/folders/lq/dh7kcps136n72nc_dhrly7nw0000gn/T/pip-install-wli41gqr/giotto-tda_6d92762b595147ea966f0f4868362d77/setup.py", line 150, in install_dependencies
      subprocess.check_call(['git', 'submodule', 'update',
    File "/Users/mbagriyanik/mambaforge/envs/ufl23/lib/python3.11/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['git', 'submodule', 'update', '--init', '--recursive']' returned non-zero exit status 128.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for giotto-tda
Running setup.py clean for giotto-tda
Failed to build giotto-tda
ERROR: Could not build wheels for giotto-tda, which is required to install pyproject.toml-based projects`

This is versions of python and packages I am using:

Python (= 3.11.2)
NumPy (=1.24.2)
SciPy (= 1.10.1)
joblib (= 1.3.0)
scikit-learn (= 1.2.2)
pyflagser (failed to install. submitted issue on pyflagser github account)
python-igraph (= 0.10.4)
plotly (= 5.15.0)
ipywidgets (= 8.0.6)

@ulupo
@mubagriyanik mubagriyanik added the bug Something isn't working label Jul 11, 2023
@mubagriyanik
Copy link
Author

giotto-ai/pyflagser#81

@noamteyssier
Copy link

Had this problem too - you can work around by using python 3.10

@mubagriyanik
Copy link
Author

mubagriyanik commented Jul 18, 2023 •
edited

Had this problem too - you can work around by using python 3.10

Thank you so much for the answer. Quick question: Only python version to change? Does that work with latest numpy or panda versions?

@noamteyssier
Copy link

Had this problem too - you can work around by using python 3.10

Thank you so much for the answer. Quick question: Only python version to change? Does that work with latest numpy or panda versions?

Didn't have any other issues - In the environment I'm using numpy==1.24.4 and pandas==2.0.3.

@lizliz
Copy link

lizliz commented Apr 19, 2024

Just wanted to bump this bug since I'm having a similar issue. Is there any plan to update giotto-tda to work with at least python 3.11?

@raphaelreinauer raphaelreinauer mentioned this issue May 29, 2024
Merged
@matteocao
Copy link
Contributor

the above should now be fixed, as we just released a novel version with supprot for python 3.11

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@lizliz @mubagriyanik @noamteyssier @matteocao