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scikit-learn-contrib / hdbscan

A high performance implementation of HDBSCAN clustering.
http://hdbscan.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
2.76k stars 497 forks source link

Can't install hdbscan in conda environment with gcc-14 #634

Open dubrsl opened 3 months ago

dubrsl commented 3 months ago

Can't install hdbscan in conda environment STR:

  1. Download and run https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  2. Create environment, update all: 
    conda create -n hdbscan
conda activate hdbscan
conda update --all
  3. Install packages:
$ conda install cython numpy scipy scikit-learn pip
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/slava/miniconda3/envs/hdbscan

  added / updated specs:
    - cython
    - numpy
    - pip
    - scikit-learn
    - scipy

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  blas               pkgs/main/linux-64::blas-1.0-mkl 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2024.3.11-h06a4308_0 
  cython             pkgs/main/linux-64::cython-3.0.10-py312h5eee18b_0 
  expat              pkgs/main/linux-64::expat-2.6.2-h6a678d5_0 
  intel-openmp       pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46306 
  joblib             pkgs/main/linux-64::joblib-1.4.0-py312h06a4308_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 
  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  mkl                pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46344 
  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py312h5eee18b_1 
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.8-py312h5eee18b_0 
  mkl_random         pkgs/main/linux-64::mkl_random-1.2.4-py312hdb19cb5_0 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  numpy              pkgs/main/linux-64::numpy-1.26.4-py312hc5e2394_0 
  numpy-base         pkgs/main/linux-64::numpy-base-1.26.4-py312h0da6c21_0 
  openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_1 
  pip                pkgs/main/linux-64::pip-24.0-py312h06a4308_0 
  pybind11-abi       pkgs/main/noarch::pybind11-abi-5-hd3eb1b0_0 
  python             pkgs/main/linux-64::python-3.12.3-h996f2a0_1 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  scikit-learn       pkgs/main/linux-64::scikit-learn-1.4.2-py312h526ad5a_1 
  scipy              pkgs/main/linux-64::scipy-1.13.0-py312hc5e2394_0 
  setuptools         pkgs/main/linux-64::setuptools-69.5.1-py312h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0 
  tbb                pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0 
  threadpoolctl      pkgs/main/noarch::threadpoolctl-2.2.0-pyh0d69192_0 
  tk                 pkgs/main/linux-64::tk-8.6.14-h39e8969_0 
  tzdata             pkgs/main/noarch::tzdata-2024a-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.43.0-py312h06a4308_0 
  xz                 pkgs/main/linux-64::xz-5.4.6-h5eee18b_1 
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1 

Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

  1. install hdbscan

    
$ LANG=C pip install hdbscan
Collecting hdbscan
Using cached hdbscan-0.8.33.tar.gz (5.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting cython<3,>=0.27 (from hdbscan)
Using cached Cython-0.29.37-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (3.1 kB)
Requirement already satisfied: numpy>=1.20 in /home/slava/miniconda3/envs/hdbscan/lib/python3.12/site-packages (from hdbscan) (1.26.4)
Requirement already satisfied: scipy>=1.0 in /home/slava/miniconda3/envs/hdbscan/lib/python3.12/site-packages (from hdbscan) (1.13.0)
Requirement already satisfied: scikit-learn>=0.20 in /home/slava/.local/lib/python3.12/site-packages (from hdbscan) (1.2.2)
Requirement already satisfied: joblib>=1.0 in /home/slava/miniconda3/envs/hdbscan/lib/python3.12/site-packages (from hdbscan) (1.4.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/slava/miniconda3/envs/hdbscan/lib/python3.12/site-packages (from scikit-learn>=0.20->hdbscan) (2.2.0)
Using cached Cython-0.29.37-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (2.0 MB)
Building wheels for collected packages: hdbscan
Building wheel for hdbscan (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for hdbscan (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [136 lines of output]
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-cpython-312
  creating build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/__init__.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/flat.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/hdbscan_.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/plots.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/prediction.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/robust_single_linkage_.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  copying hdbscan/validity.py -> build/lib.linux-x86_64-cpython-312/hdbscan
  creating build/lib.linux-x86_64-cpython-312/hdbscan/tests
  copying hdbscan/tests/__init__.py -> build/lib.linux-x86_64-cpython-312/hdbscan/tests
  copying hdbscan/tests/test_flat.py -> build/lib.linux-x86_64-cpython-312/hdbscan/tests
  copying hdbscan/tests/test_hdbscan.py -> build/lib.linux-x86_64-cpython-312/hdbscan/tests
  copying hdbscan/tests/test_prediction_utils.py -> build/lib.linux-x86_64-cpython-312/hdbscan/tests
  copying hdbscan/tests/test_rsl.py -> build/lib.linux-x86_64-cpython-312/hdbscan/tests
  running build_ext
  cythoning hdbscan/_hdbscan_tree.pyx to hdbscan/_hdbscan_tree.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/_hdbscan_tree.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning hdbscan/_hdbscan_linkage.pyx to hdbscan/_hdbscan_linkage.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/_hdbscan_linkage.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning hdbscan/_hdbscan_boruvka.pyx to hdbscan/_hdbscan_boruvka.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/_hdbscan_boruvka.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning hdbscan/_hdbscan_reachability.pyx to hdbscan/_hdbscan_reachability.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/_hdbscan_reachability.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning hdbscan/_prediction_utils.pyx to hdbscan/_prediction_utils.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/_prediction_utils.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning hdbscan/dist_metrics.pyx to hdbscan/dist_metrics.c
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/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: /tmp/pip-install-__v1ce2i/hdbscan_690bcb27b9474f6087a9bb44381d8770/hdbscan/dist_metrics.pxd
    tree = Parsing.p_module(s, pxd, full_module_name)
  building 'hdbscan._hdbscan_tree' extension
  creating build/temp.linux-x86_64-cpython-312
  creating build/temp.linux-x86_64-cpython-312/hdbscan
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/_hdbscan_tree.c -o build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_tree.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/_hdbscan_tree.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -shared -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_tree.o -o build/lib.linux-x86_64-cpython-312/hdbscan/_hdbscan_tree.cpython-312-x86_64-linux-gnu.so
  building 'hdbscan._hdbscan_linkage' extension
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/_hdbscan_linkage.c -o build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_linkage.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/_hdbscan_linkage.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -shared -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_linkage.o -o build/lib.linux-x86_64-cpython-312/hdbscan/_hdbscan_linkage.cpython-312-x86_64-linux-gnu.so
  building 'hdbscan._hdbscan_boruvka' extension
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/_hdbscan_boruvka.c -o build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_boruvka.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/_hdbscan_boruvka.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -shared -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_boruvka.o -o build/lib.linux-x86_64-cpython-312/hdbscan/_hdbscan_boruvka.cpython-312-x86_64-linux-gnu.so
  building 'hdbscan._hdbscan_reachability' extension
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/_hdbscan_reachability.c -o build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_reachability.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/_hdbscan_reachability.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -shared -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib build/temp.linux-x86_64-cpython-312/hdbscan/_hdbscan_reachability.o -o build/lib.linux-x86_64-cpython-312/hdbscan/_hdbscan_reachability.cpython-312-x86_64-linux-gnu.so
  building 'hdbscan._prediction_utils' extension
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/_prediction_utils.c -o build/temp.linux-x86_64-cpython-312/hdbscan/_prediction_utils.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/_prediction_utils.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -shared -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath,/home/slava/miniconda3/envs/hdbscan/lib -Wl,-rpath-link,/home/slava/miniconda3/envs/hdbscan/lib -L/home/slava/miniconda3/envs/hdbscan/lib build/temp.linux-x86_64-cpython-312/hdbscan/_prediction_utils.o -o build/lib.linux-x86_64-cpython-312/hdbscan/_prediction_utils.cpython-312-x86_64-linux-gnu.so
  building 'hdbscan.dist_metrics' extension
  gcc -pthread -B /home/slava/miniconda3/envs/hdbscan/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -O2 -isystem /home/slava/miniconda3/envs/hdbscan/include -fPIC -I/home/slava/miniconda3/envs/hdbscan/include/python3.12 -I/tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include -c hdbscan/dist_metrics.c -o build/temp.linux-x86_64-cpython-312/hdbscan/dist_metrics.o
  In file included from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from hdbscan/dist_metrics.c:752:
  /tmp/pip-build-env-8zan49bl/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  hdbscan/dist_metrics.c: In function ‘__pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_dist’:
  hdbscan/dist_metrics.c:7333:75: error: passing argument 1 of ‘__pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
   7333 |   __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 474, __pyx_L1_error)
        |                                                                          ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                                                           |
        |                                                                           struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *
  hdbscan/dist_metrics.c:7130:168: note: expected ‘struct __pyx_obj_7hdbscan_12dist_metrics_SEuclideanDistance *’ but argument is of type ‘struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *’
   7130 | static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_SEuclideanDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) {
        |                                                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  hdbscan/dist_metrics.c: In function ‘__pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_dist’:
  hdbscan/dist_metrics.c:8109:74: error: passing argument 1 of ‘__pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
   8109 |   __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 563, __pyx_L1_error)
        |                                                                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                                                          |
        |                                                                          struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *
  hdbscan/dist_metrics.c:8025:166: note: expected ‘struct __pyx_obj_7hdbscan_12dist_metrics_MinkowskiDistance *’ but argument is of type ‘struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *’
   8025 | static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_MinkowskiDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) {
        |                                                                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  hdbscan/dist_metrics.c: In function ‘__pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_dist’:
  hdbscan/dist_metrics.c:8807:75: error: passing argument 1 of ‘__pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
   8807 |   __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 622, __pyx_L1_error)
        |                                                                          ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                                                           |
        |                                                                           struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *
  hdbscan/dist_metrics.c:8614:168: note: expected ‘struct __pyx_obj_7hdbscan_12dist_metrics_WMinkowskiDistance *’ but argument is of type ‘struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *’
   8614 | static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_WMinkowskiDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) {
        |                                                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  hdbscan/dist_metrics.c: In function ‘__pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_dist’:
  hdbscan/dist_metrics.c:9636:76: error: passing argument 1 of ‘__pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
   9636 |   __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 692, __pyx_L1_error)
        |                                                                           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                                                            |
        |                                                                            struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *
  hdbscan/dist_metrics.c:9385:170: note: expected ‘struct __pyx_obj_7hdbscan_12dist_metrics_MahalanobisDistance *’ but argument is of type ‘struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *’
   9385 | static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_MahalanobisDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) {
        |                                                                                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  error: command '/usr/bin/gcc' 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 hdbscan
Failed to build hdbscan
ERROR: Could not build wheels for hdbscan, which is required to install pyproject.toml-based projects

Expected result: the package will be installed.
dubrsl commented 3 months ago

With compiler version 13.2 the problem was solved:

conda config --add channels conda-forg
conda install gcc_linux-64=13.2.0
reuning commented 3 months ago

FWIW, I had the same issue but was able to get hdbscan to build by using Cython 3 but then saw that there are other incompatibility issues

levnikmyskin commented 2 months ago

This is also happening on Archlinux (or I guess, any distro using gcc 14).

On Arch, this can be fixed by running:

sudo pacman -S gcc13
CC=/usr/bin/gcc-13 pip install hdbscan