8000 Compiling Fails due to sklearn/metrics/pairwise.py · Issue #29757 · scikit-learn/scikit-learn · GitHub
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conradstevens opened this issue Aug 31, 2024 · 8 comments
Closed

Compiling Fails due to sklearn/metrics/pairwise.py #29757

conradstevens opened this issue Aug 31, 2024 · 8 comments
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@conradstevens
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conradstevens commented Aug 31, 2024 •
edited by glemaitre
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Describe the bug

This may be a duplicate of 29754.

Having merged from upstream, the imports in sklearn/metrics/pairwise.py do not compile.

I am getting error:
"sklearn/metrics/_dist_metrics.pyx", line 1, in init sklearn.metrics._dist_metrics"

I have tried rebuilding my conda environment and sklearn.

Steps/Code to Reproduce

$ python -m sklearn.kernel_approximation

Expected Results

not an error

Actual Results

Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/Users/conradstevens/scikit-learn/sklearn/kernel_approximation.py", line 20, in <module>
    from .metrics.pairwise import KERNEL_PARAMS, PAIRWISE_KERNEL_FUNCTIONS, pairwise_kernels
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/__init__.py", line 6, in <module>
    from . import cluster
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/cluster/__init__.py", line 28, in <module>
    from ._unsupervised import (
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/cluster/_unsupervised.py", line 21, in <module>
    from ..pairwise import _VALID_METRICS, pairwise_distances, pairwise_distances_chunked
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/pairwise.py", line 46, in <module>
    from ._pairwise_distances_reduction import ArgKmin
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/_pairwise_distances_reduction/__init__.py", line 97, in <module>
    from ._dispatcher import (
  File "/Users/conradstevens/scikit-learn/sklearn/metrics/_pairwise_distances_reduction/_dispatcher.py", line 11, in <module>
    from .._dist_metrics import (
  File "sklearn/metrics/_dist_metrics.pyx", line 1, in init sklearn.metrics._dist_metrics
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Versions

$ python -c "import sklearn; sklearn.show_versions()"

System:
    python: 3.12.5 | packaged by conda-forge | (main, Aug  8 2024, 18:31:54) [Clang 16.0.6 ]
executable: /opt/homebrew/Caskroom/miniconda/base/envs/sklearn-dev-3/bin/python
   machine: macOS-14.4.1-x86_64-i386-64bit

Python dependencies:
      sklearn: 1.6.dev0
          pip: 24.2
   setuptools: 72.2.0
        numpy: 2.1.0
        scipy: 1.14.1
       Cython: 3.0.11
       pandas: None
   matplotlib: None
       joblib: 1.4.2
threadpoolctl: 3.5.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
    num_threads: 10
         prefix: libopenblas
       filepath: /opt/homebrew/Caskroom/miniconda/base/envs/sklearn-dev-3/lib/libopenblasp-r0.3.27.dylib
        version: 0.3.27
threading_layer: openmp
   architecture: Nehalem

       user_api: openmp
   internal_api: openmp
    num_threads: 10
         prefix: libomp
       filepath: /opt/homebrew/Caskroom/miniconda/base/envs/sklearn-dev-3/lib/libomp.dylib
        version: None
@conradstevens conradstevens added Bug Needs Triage Issue requires triage labels Aug 31, 2024
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@glemaitre
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This is not related to #29754. The latter issue is related the wheels building and fail for Windows while you are under MacOS.

The error that you witness is related to numpy/numpy#26710. I'm a bit confused why you get it with the development version. Normally, the error is triggered when you have NumPy 2.0+ with an older version of scikit-learn that is not compatible with NumPy 2.0+.

Could you retry to clean and rebuild from source with shown dependencies.

@glemaitre glemaitre removed the Needs Triage Issue requires triage label Aug 31, 2024
@conradstevens
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conradstevens commented Aug 31, 2024 •
edited by glemaitre
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Thank you @glemaitre I have rebuild from source and getting the same issue.
I am not entirely sure what you mean by 'with shown dependencies'. Below is what is in my conda environment:

\# packages in environment at /opt/homebrew/Caskroom/miniconda/base/envs/sklearn-dev-5:
\#
\# Name                    Version                   Build  Channel
bzip2                     1.0.8                hfdf4475_7    conda-forge
c-compiler                1.7.0                h282daa2_1    conda-forge
ca-certificates           2024.8.30            h8857fd0_0    conda-forge
cctools                   986                  h40f6528_3    conda-forge
cctools_osx-64            986                  h303a5ab_3    conda-forge
clang                     16.0.6          default_h179603d_13    conda-forge
clang-16                  16.0.6          default_h0c94c6a_13    conda-forge
clang_impl_osx-64         16.0.6              h8787910_19    conda-forge
clang_osx-64              16.0.6              hb91bd55_19    conda-forge
clangxx                   16.0.6          default_h179603d_13    conda-forge
clangxx_impl_osx-64       16.0.6              h6d92fbe_19    conda-forge
clangxx_osx-64            16.0.6              hb91bd55_19    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-fo
8000
rge
compiler-rt               16.0.6               ha38d28d_2    conda-forge
compiler-rt_osx-64        16.0.6               ha38d28d_2    conda-forge
compilers                 1.7.0                h694c41f_1    conda-forge
cxx-compiler              1.7.0                h7728843_1    conda-forge
cython                    3.0.11          py312h5861a67_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
fortran-compiler          1.7.0                h6c2ab21_1    conda-forge
gfortran                  12.3.0               h2c809b3_1    conda-forge
gfortran_impl_osx-64      12.3.0               hc328e78_3    conda-forge
gfortran_osx-64           12.3.0               h18f7dce_1    conda-forge
gmp                       6.3.0                hf036a51_2    conda-forge
icu                       75.1                 h120a0e1_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
isl                       0.26            imath32_h2e86a7b_101    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
ld64                      711                  ha02d983_3    conda-forge
ld64_osx-64               711                  h04ffbf3_3    conda-forge
libblas                   3.9.0           22_osx64_openblas    conda-forge
libcblas                  3.9.0           22_osx64_openblas    conda-forge
libclang-cpp16            16.0.6          default_h0c94c6a_13    conda-forge
libcxx                    18.1.8               hd876a4e_6    conda-forge
libcxx-devel              16.0.6               h8f8a49f_2    conda-forge
libexpat                  2.6.2                h73e2aa4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran-devel_osx-64  12.3.0               h0b6f5ec_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
liblapack                 3.9.0           22_osx64_openblas    conda-forge
libllvm16                 16.0.6               hbedff68_3    conda-forge
libopenblas               0.3.27          openmp_h8869122_1    conda-forge
libsqlite                 3.46.0               h1b8f9f3_0    conda-forge
libxml2                   2.12.7               heaf3512_4    conda-forge
libzlib                   1.3.1                h87427d6_1    conda-forge
llvm-openmp               18.1.8               h15ab845_1    conda-forge
llvm-tools                16.0.6               hbedff68_3    conda-forge
meson                     1.5.1              pyhd8ed1ab_1    conda-forge
meson-python              0.16.0             pyh0c530f3_0    conda-forge
mpc                       1.3.1                h9d8efa1_0    conda-forge
mpfr                      4.2.1                hc80595b_2    conda-forge
ncurses                   6.5                  hf036a51_1    conda-forge
ninja                     1.12.1               h3c5361c_0    conda-forge
numpy                     2.1.0           py312h8813227_0    conda-forge
openssl                   3.3.1                hd23fc13_3    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pip                       24.2               pyh8b19718_1    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
pyproject-metadata        0.8.0              pyhd8ed1ab_0    conda-forge
pytest                    8.3.2              pyhd8ed1ab_0    conda-forge
python                    3.12.5          h37a9e06_0_cpython    conda-forge
python_abi                3.12                    5_cp312    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
scikit-learn              1.6.dev0                 pypi_0    pypi
scipy                     1.14.1          py312he82a568_0    conda-forge
setuptools                72.2.0             pyhd8ed1ab_0    conda-forge
sigtool                   0.1.3                h88f4db0_0    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h8827d51_1    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
zlib                      1.3.1                h87427d6_1    conda-forge
zstd                      1.5.6                h915ae27_0    conda-forge

When compiling I get warning:

[139/251] Compiling C object sklearn/metrics/_dist_metrics.cpython-312-darwin.so.p/meson-generated_sklearn_metrics__dist_metrics.pyx.c.o
  sklearn/metrics/_dist_metrics.cpython-312-darwin.so.p/sklearn/metrics/_dist_metrics.pyx.c:29538:29: warning: assigning to '__pyx_t_7sklearn_5utils_9_typedefs_float64_t *' (aka 'double *') from 'const __pyx_t_7sklearn_5utils_9_typedefs_float64_t *' (aka 'const double *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
              __pyx_v_x2_data = ((&(*((__pyx_t_7sklearn_5utils_9_typedefs_float64_t const  *) ( /* dim=1 */ ((char *) (((__pyx_t_7sklearn_5utils_9_typedefs_float64_t const  *) ( /* dim=0 */ (__pyx_v_Y_data.data + __pyx_t_18 * __pyx_v_Y_data.strides[0]) )) + __pyx_t_19)) )))) + (__pyx_v_i2 * __pyx_v_n_features));

@conradstevens conradstevens mentioned this issue Sep 1, 2024
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@lesteve
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lesteve commented Sep 1, 2024

It's hard to tell what is happening but I am pretty sure that this should go away if you rebuild from scratch. Try something like this before rebuilding:

rm -rf build
git clean -xdf

@glemaitre
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When compiling I get warning:

Don't worry about the warning, this should not be an issue. We have a several PRs that tries to reduce the number of warnings in the past.

@conradstevens
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It's hard to tell what is happening but I am pretty sure that this should go away if you rebuild from scratch. Try something like this before rebuilding:

rm -rf build
git clean -xdf

It seems this fixed it. Thank you all

@lesteve lesteve added Question and removed Bug labels Sep 1, 2024
@lesteve
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lesteve commented Sep 1, 2024 •
edited
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Great to hear that 🎉. It can happen to be in weird situations like this and the rebuild from scratch is the first thing to try ...

It's a bit hard at the beginning but after a bit of time you will get some intuition whether something is likely due to scikit-learn or to your local setup somehow. In this particular case, we have tests running on each commit on a variety of platforms so it was quite unlikely that it was a scikit-learn issue or we would likely have noticed.

Having said that, it can happen that main is broken, maybe once every 6 months or so, so if you notice something that does not go away after a rebuild from scratch, do open an issue!

In your particular case, I am guessing that what happened is that you built with numpy<2 and then upgraded your environment to numpy>=2. This is a known issue that in this case you will get a not so user-friendly error message unfortunately see https://numpy.org/devdocs/user/troubleshooting-importerror.html#downstream-importerror-attributeerror-or-c-api-abi-incompatibility for more details.

@lesteve lesteve closed this as completed Sep 1, 2024
@hlin-0420
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I am using windows for installing goldenverba, and encountered the following similar error with preparing the meta data:

Preparing metadata (pyproject.toml) ... error

Steps/Code to Reproduce

pip install goldenverba

Expected

No errors: a successful installation.

Actual Result:

error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [124 lines of output]
      + meson setup C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba\.mesonpy-1x4b5lnb -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba\.mesonpy-1x4b5lnb\meson-python-native-file.ini
      The Meson build system
      Version: 1.7.0
      Source dir: C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba
      Build dir: C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba\.mesonpy-1x4b5lnb
      Build type: native build
      Project name: scikit-learn
      Project version: 1.5.1
      Activating VS 17.12.4
      C compiler for the host machine: cl (msvc 19.42.34436 "Microsoft (R) C/C++ Optimizing Compiler Version 19.42.34436 for x64")
      C linker for the host machine: link link 14.42.34436.0
      C++ compiler for the host machine: cl (msvc 19.42.34436 "Microsoft (R) C/C++ Optimizing Compiler Version 19.42.34436 for x64")
      C++ linker for the host machine: link link 14.42.34436.0
      Cython compiler for the host machine: cython (cython 3.0.12)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Compiler for C supports arguments -Wno-unused-but-set-variable: NO
      Compiler for C supports arguments -Wno-unused-function: NO
      Compiler for C supports arguments -Wno-conversion: NO
      Compiler for C supports arguments -Wno-misleading-indentation: NO
      Library m found: NO
      Program python found: YES (C:\Users\HaochengLin\Desktop\Verba-Model\venv\Scripts\python.exe)
      Run-time dependency OpenMP for c found: YES 2.0
      Run-time dependency python found: YES 3.13
      Build targets in project: 111

      scikit-learn 1.5.1

        User defined options
          Native files: C:\Users\HaochengLin\AppData\Local\Temp\pip-install-7c4qw_4k\scikit-learn_715436ce7c184007ab495e4d6782f6ba\.mesonpy-1x4b5lnb\meson-python-native-file.ini
          b_ndebug    : if-release
          b_vscrt     : md
          buildtype   : release

      Found ninja.EXE-1.11.1.git.kitware.jobserver-1 at C:\Users\HaochengLin\AppData\Local\Programs\Python\Python313\Scripts\ninja.EXE
      + meson compile
      [1/249] Generating sklearn/write_built_with_meson_file with a custom command
      [2/249] Generating sklearn/utils/_seq_dataset_pxd with a custom command
      [3/249] Generating sklearn/utils/_weight_vector_pxd with a custom command
      [4/249] Copying file sklearn/utils/_cython_blas.pxd
      [5/249] Generating sklearn/metrics/_dist_metrics_pxd with a custom command
      [6/249] Copying file sklearn/utils/_random.pxd
      [7/249] Copying file sklearn/__init__.py
      [8/249] Copying file sklearn/utils/__init__.py
      [9/249] Copying file sklearn/utils/_sorting.pxd
      [10/249] Copying file sklearn/_loss/_loss.pxd
      [11/249] Copying file sklearn/utils/_typedefs.pxd
      [12/249] Copying file sklearn/utils/_openmp_helpers.pxd
      [13/249] Copying file sklearn/utils/_heap.pxd
      [14/249] Copying file sklearn/utils/_vector_sentinel.pxd
      [15/249] Generating sklearn/metrics/_pairwise_distances_reduction/_base_pxd with a custom command
      [16/249] Generating sklearn/metrics/_pairwise_distances_reduction/_datasets_pair_pxd with a custom command
      [17/249] Generating sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer_pxd with a custom command
      [18/249] Copying file sklearn/metrics/__init__.py
      [19/249] Generating sklearn/metrics/_pairwise_distances_reduction/_argkmin_pxd with a custom command
      [20/249] Generating sklearn/_loss/_loss_pyx with a custom command
      [21/249] Generating sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_pxd with a custom command
      [22/249] Compiling C++ object sklearn/utils/murmurhash.cp313-win_amd64.pyd.p/src_MurmurHash3.cpp.obj
      [23/249] Copying file sklearn/metrics/_pairwise_distances_reduction/_classmode.pxd
      [24/249] Copying file sklearn/metrics/_pairwise_distances_reduction/__init__.py
      [25/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/__check_build/_check_build.pyx
      [26/249] Compiling C object sklearn/__check_build/_check_build.cp313-win_amd64.pyd.p/meson-generated_sklearn___check_build__check_build.pyx.c.obj
      [27/249] Linking target sklearn/__check_build/_check_build.cp313-win_amd64.pyd
         Creating library sklearn\__check_build\_check_build.cp313-win_amd64.lib and object sklearn\__check_build\_check_build.cp313-win_amd64.exp

      [28/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/_isotonic.pyx
      [29/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_heap.pyx
      [30/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_openmp_helpers.pyx
      [31/249] Compiling C object sklearn/utils/_heap.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__heap.pyx.c.obj
      [32/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/murmurhash.pyx
      [33/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/metrics/cluster/_expected_mutual_info_fast.pyx
      [34/249] Compiling C object sklearn/utils/_openmp_helpers.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__openmp_helpers.pyx.c.obj
      [35/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_typedefs.pyx
      [36/249] Linking target sklearn/utils/_heap.cp313-win_amd64.pyd
         Creating library sklearn\utils\_heap.cp313-win_amd64.lib and object sklearn\utils\_heap.cp313-win_amd64.exp

      [37/249] Linking target sklearn/utils/_openmp_helpers.cp313-win_amd64.pyd
         Creating library sklearn\utils\_openmp_helpers.cp313-win_amd64.lib and object sklearn\utils\_openmp_helpers.cp313-win_amd64.exp

      [38/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_fast_dict.pyx
      [39/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_random.pyx
      [40/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/cluster/_hdbscan/_reachability.pyx
      [41/249] Generating sklearn/utils/_seq_dataset_pyx with a custom command
      [42/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_sorting.pyx
      [43/249] Compiling C object sklearn/_isotonic.cp313-win_amd64.pyd.p/meson-generated_sklearn__isotonic.pyx.c.obj
      [44/249] Generating sklearn/utils/_weight_vector_pyx with a custom command
      [45/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_cython_blas.pyx
      [46/249] Compiling C object sklearn/utils/murmurhash.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils_murmurhash.pyx.c.obj
      ..\sklearn\utils\src/MurmurHash3.h(16): warning C4142: 'uint32_t': benign redefinition of type
      C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.42.34433\include\stdint.h(24): note: see declaration of 'uint32_t'
      [47/249] Compiling C object sklearn/utils/_sorting.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__sorting.pyx.c.obj
      [48/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/sparsefuncs_fast.pyx
      [49/249] Compiling C object sklearn/utils/_typedefs.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__typedefs.pyx.c.obj
      [50/249] Compiling C object sklearn/utils/_random.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__random.pyx.c.obj
      [51/249] Compiling C++ object sklearn/utils/_fast_dict.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__fast_dict.pyx.cpp.obj
      sklearn/utils/_fast_dict.cp313-win_amd64.pyd.p/sklearn/utils/_fast_dict.pyx.cpp(26950): warning C4551: function call missing argument list
      sklearn/utils/_fast_dict.cp313-win_amd64.pyd.p/sklearn/utils/_fast_dict.pyx.cpp(30800): warning C4551: function call missing argument list
      sklearn/utils/_fast_dict.cp313-win_amd64.pyd.p/sklearn/utils/_fast_dict.pyx.cpp(30801): warning C4551: function call missing argument list
      sklearn/utils/_fast_dict.cp313-win_amd64.pyd.p/sklearn/utils/_fast_dict.pyx.cpp(30802): warning C4551: function call missing argument list
      [52/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_vector_sentinel.pyx
      [53/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/_isfinite.pyx
      [54/249] Compiling Cython source C:/Users/HaochengLin/AppData/Local/Temp/pip-install-7c4qw_4k/scikit-learn_715436ce7c184007ab495e4d6782f6ba/sklearn/utils/arrayfuncs.pyx
      [55/249] Compiling Cython source sklearn/utils/_weight_vector.pyx
      [56/249] Compiling Cython source sklearn/utils/_seq_dataset.pyx
      [57/249] Compiling C++ object sklearn/utils/_vector_sentinel.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__vector_sentinel.pyx.cpp.obj
      sklearn/utils/_vector_sentinel.cp313-win_amd64.pyd.p/sklearn/utils/_vector_sentinel.pyx.cpp(15416): warning C4551: function call missing argument list
      [58/249] Linking target sklearn/utils/murmurhash.cp313-win_amd64.pyd
         Creating library sklearn\utils\murmurhash.cp313-win_amd64.lib and object sklearn\utils\murmurhash.cp313-win_amd64.exp

      [59/249] Linking target sklearn/_isotonic.cp313-win_amd64.pyd
         Creating library sklearn\_isotonic.cp313-win_amd64.lib and object sklearn\_isotonic.cp313-win_amd64.exp

      [60/249] Linking target sklearn/utils/_typedefs.cp313-win_amd64.pyd
         Creating library sklearn\utils\_typedefs.cp313-win_amd64.lib and object sklearn\utils\_typedefs.cp313-win_amd64.exp

      [61/249] Generating sklearn/metrics/_dist_metrics_pyx with a custom command
      [62/249] Coninja: error: mkdir(sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.cp313-win_amd64.pyd.p/sklearn/metrics/_pairwise_distances_reduction): No such file or directory
      mpiling C object sklearn/utils/_cython_blas.cp313-win_amd64.pyd.p/meson-generated_sklearn_utils__cython_blas.pyx.c.obj
      [63/249] Generating sklearn/metrics/_pairwise_distances_reduction/_datasets_pair_pyx with a custom command
      ninja: build stopped: .
      Activating VS 17.12.4
      INFO: automatically activated MSVC compiler environment
      INFO: autodetecting backend as ninja
      INFO: calculating backend command to run: C:\Users\HaochengLin\AppData\Local\Programs\Python\Python313\Scripts\ninja.EXE
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

Would you like to check to see if this issue could be resolved or reproduced?

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@lesteve @conradstevens @glemaitre @torinriley @hlin-0420
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