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ERROR: Could not build wheels for brainiak, which is required to install pyproject.toml-based projects #509

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ERROR: Could not build wheels for brainiak, which is required to install pyproject.toml-based projects#509

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@orenpapers
orenpapers
opened on Jan 23, 2022

Hi,
I am using MACOS Catalina 10.15.
I want to install Brainiak.
I followed to instructions here:
https://brainiak.org/docs/installation.html
But I get an error for python3 -m pip install -U brainiak:

  ERROR: Command errored out with exit status 1:
   command: /<path>/venv_3.8/bin/python3 /<path>/venv_3.8/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmpfqcg0urs
       cwd: /private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-install-99egj3s0/brainiak_9b1ca70a75954854ba9ad223ace38081
  Complete output (89 lines):
  running bdist_wheel
  running build
  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/brainiak
  copying brainiak/isc.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak
  copying brainiak/io.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak
  copying brainiak/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak
  copying brainiak/image.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/searchlight
  copying brainiak/searchlight/searchlight.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/searchlight
  copying brainiak/searchlight/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/searchlight
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/hyperparamopt
  copying brainiak/hyperparamopt/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/hyperparamopt
  copying brainiak/hyperparamopt/hpo.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/hyperparamopt
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  copying brainiak/funcalign/fastsrm.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  copying brainiak/funcalign/sssrm.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  copying brainiak/funcalign/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  copying brainiak/funcalign/rsrm.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  copying brainiak/funcalign/srm.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/funcalign
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/covs.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/regression.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/matnormal_likelihoods.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/mnrsa.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  copying brainiak/matnormal/utils.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/matnormal
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  copying brainiak/factoranalysis/tfa.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  copying brainiak/factoranalysis/htfa.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  copying brainiak/factoranalysis/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/mvpa_voxelselector.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/classifier.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/util.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/preprocessing.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  copying brainiak/fcma/voxelselector.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/reprsimil
  copying brainiak/reprsimil/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/reprsimil
  copying brainiak/reprsimil/brsa.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/reprsimil
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  copying brainiak/utils/fmrisim_real_time_generator.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  copying brainiak/utils/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  copying brainiak/utils/fmrisim.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  copying brainiak/utils/utils.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  copying brainiak/utils/kronecker_solvers.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/reconstruct
  copying brainiak/reconstruct/iem.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/reconstruct
  copying brainiak/reconstruct/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/reconstruct
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/eventseg
  copying brainiak/eventseg/event.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/eventseg
  copying brainiak/eventseg/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/brainiak/eventseg
  running egg_info
  listing git files failed - pretending there aren't any
  writing manifest file 'brainiak.egg-info/SOURCES.txt'
  copying brainiak/factoranalysis/tfa_extension.cpp -> build/lib.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  copying brainiak/fcma/cython_blas.pyx -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma/src
  copying brainiak/fcma/src/fcma_extension.cc -> build/lib.macosx-10.9-x86_64-3.8/brainiak/fcma/src
  creating build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/utils/sim_parameters/ROI_A.nii.gz -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/utils/sim_parameters/ROI_B.nii.gz -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/utils/sim_parameters/grey_matter_mask.npy -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/utils/sim_parameters/sub_noise_dict.txt -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/utils/sim_parameters/sub_template.nii.gz -> build/lib.macosx-10.9-x86_64-3.8/brainiak/utils/sim_parameters
  copying brainiak/eventseg/_utils.pyx -> build/lib.macosx-10.9-x86_64-3.8/brainiak/eventseg
  running build_ext
  creating var
  creating var/folders
  creating var/folders/39
  creating var/folders/39/88clnp910zlg54lrgy0d7qm40000gn
  creating var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/<path>venv_3.8/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -c /var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmpl9ppzse1.cpp -o var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmpl9ppzse1.o -std=c++14
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/<path>/venv_3.8/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -c /var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmpctn4d8qj.cpp -o var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmpctn4d8qj.o -std=c++14
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/<path>/venv_3.8/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -c /var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmp_4grir9f.cpp -o var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmp_4grir9f.o -std=c++14
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/<path>/venv_3.8/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -c /var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmp1nvpvxwv.cpp -o var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/tmp1nvpvxwv.o -std=c++14
  creating build/temp.macosx-10.9-x86_64-3.8
  creating build/temp.macosx-10.9-x86_64-3.8/brainiak
  creating build/temp.macosx-10.9-x86_64-3.8/brainiak/factoranalysis
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/<path>/venv_3.8/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -I/private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/pybind11/include -c brainiak/factoranalysis/tfa_extension.cpp -o build/temp.macosx-10.9-x86_64-3.8/brainiak/factoranalysis/tfa_extension.o -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO=\"0.11\" -std=c++14
  clang: error: unsupported option '-fopenmp'
  /private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-install-99egj3s0/brainiak_9b1ca70a75954854ba9ad223ace38081/brainiak/fcma/cython_blas.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  /private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-build-env-rv0h7kfm/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/39/88clnp910zlg54lrgy0d7qm40000gn/T/pip-install-99egj3s0/brainiak_9b1ca70a75954854ba9ad223ace38081/brainiak/eventseg/_utils.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for brainiak
Failed to build brainiak
ERROR: Could not build wheels for brainiak, which is required to install pyproject.toml-based projects

Any idea why or what can I do?

Activity

  1. mihaic commented on Jan 24, 2022

    @mihaic
    mihaic
    on Jan 24, 2022
    Member

    Hello, @orko19! It looks like BrainIAK is using a clang that does not support OpenMP. You probably noticed in the BrainIAK installation instructions you linked a section about installing LLVM with brew and setting up your environment:

    You must instruct programs to use this clang version at /usr/local/opt/llvm/bin. One way to do this, which works for most programs, is setting the CC environment variable. You can add the following lines to $HOME/.profile (or $HOME/.bash_profile, if you have one). For them to take effect, you must logout or launch a new login shell, e.g., bash -l:

    export CC=/usr/local/opt/llvm/bin/clang
    export CXX=/usr/local/opt/llvm/bin/clang++

    In addition, you also need to specify the directories that the newly installed clang will seek for compiling and linking:

    export LDFLAGS="-L/usr/local/opt/llvm/lib "
    "-Wl,-rpath,/usr/local/opt/llvm/lib $LDFLAGS"
    export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"

    If you followed those instructions, you should see the LLVM you install when running the following command:

    echo $CC

  2. orenpapers commented on Jan 24, 2022

    @orenpapers
    orenpapers
    on Jan 24, 2022
    Author

    @mihaic Thanks!
    Please see my ~/.bash_profile, I do have these lines:
    image

    And when I write echo $CC
    I do get this result:
    /usr/local/opt/llvm/bin/clang
    Any idea?

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