BUG: Build from source can fail  on Windows for scikit-learn v1.6.1 with Ninja `mkdir` error

**Labels:** `Bug`, `Build / CI`, `Needs Triage` (Suggested)

**Describe the bug**

Scikit-learn (v1.6.1) fails to build from source on a native Windows 11 ARM64 machine using the MSYS2 ClangARM64 toolchain. The build proceeds through the Meson setup phase correctly identifying the `clang` compiler, but fails during the `ninja` compilation phase with an error indicating it cannot create a specific, deeply nested intermediate build directory.

This occurs despite successfully building other complex dependencies like NumPy (v2.2.4) and SciPy (v1.15.2) from source in the *exact same environment*. Pandas (v2.2.3) also builds successfully after setting `MESON_DISABLE_VSENV=1` (otherwise it incorrectly selects MSVC). This suggests the issue might be specific to how scikit-learn's build structure interacts with Meson/Ninja within this particular toolchain environment.

This is related to, but distinct from, #30567 which requests pre-built wheels. This issue focuses on a specific build-from-source failure.

**Steps/Code to Reproduce**

1.  **Environment Setup:**
    *   OS: Windows 11 Pro ARM64 (via Parallels on Apple Silicon M2, or on native hardware like Windows Dev Kit 2023)
    *   MSYS2: Latest version, updated via `pacman -Syu`.
    *   MSYS2 Environment: `CLANGARM64` shell launched.
    *   Key MSYS2 Packages (installed via `pacman -S mingw-w64-clang-aarch64-<package>`):
        *   `python` (3.12.x)
        *   `clang` (20.1.1)
        *   `flang` (20.1.1)
        *   `meson` (1.7.0)
        *   `ninja` (1.12.1)
        *   `pkgconf`
        *   `openblas`
        *   `lapack`
        *   `openssl`
        *   `hdf5`
        *   `rust`
        *   `zlib`
    *   Project Location: Tried both native MSYS2 path (`/home/user/project`) and WSL interop path (`//wsl.localhost/Ubuntu/...`) - error persists in both.

2.  **Python Virtual Environment:**
    ```bash
    # In CLANGARM64 shell, navigate to project directory
    python -m venv .venv
    source .venv/bin/activate # Or Scripts/activate
    python -m pip install --upgrade pip setuptools wheel
    ```

3.  **Environment Variables:** Before attempting install, set the following in the activated CLANGARM64 shell:
    ```bash
    # Unset potential conflicts
    unset CL _CL_ OPENSSL_LIB_DIR OPENSSL_INCLUDE_DIR OPENSSL_DIR

    # Set compilers (though often picked up correctly by MSYS2 shell)
    export CC=clang
    export CXX=clang++

    # Attempt to prevent Meson from activating MSVC (worked for Pandas)
    export MESON_DISABLE_VSENV=1

    # Ensure pkg-config uses MSYS2 paths
    export PKG_CONFIG_PATH="/clangarm64/lib/pkgconfig:/clangarm64/share/pkgconfig"

    # Attempt to use short temporary paths (tried /tmp and C:/pip_build_temp)
    export TMPDIR="C:/pip_build_temp" # Or /tmp
    mkdir -p $TMPDIR
    ```

4.  **Attempt Installation:**
    ```bash
    python -m pip install --verbose scikit-learn==1.6.1
    # (Or use `pip install -r requirements.txt` containing scikit-learn==1.6.1)
    ```

**Expected Results**

Scikit-learn==1.6.1 should build and install successfully, similar to how NumPy and SciPy do in the same configured environment.

**Actual Results**

The build process starts, Meson correctly identifies `clang`, dependencies are resolved, Cython files are processed, but compilation fails during the Ninja execution phase.

The key error message is:
```
[...]
[48/251] Compiling Cython source C:/pip_build_temp/pip-install-.../scikit-learn.../utils/_fast_dict.pyx
ninja: error: mkdir(sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cp312-mingw_aarch64_ucrt_llvm.pyd.p/sklearn/metrics/_pairwise_distances_reduction): No such file or directory
ninja: build stopped: .
[...]
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
[...]
error: metadata-generation-failed
```

*(Note: The exact file being compiled just before the error ([48/251] in the log provided previously) might vary slightly, but the `ninja: error: mkdir(...)` is consistent).*
<details><summary>full log</summary><p>

## full error trace
```
@energypc CLANGARM64 ~/projects_msys/func-ecopower-pwm-forecast-durable
$ python -m pip install --verbose scikit-learn==1.6.1
Using pip 25.0.1 from C:/msys64/home/oscar/projects_msys/func-ecopower-pwm-forecast-durable/.venv/lib/python3.12/site-packages/pip (python 3.12)
Collecting scikit-learn==1.6.1
  Using cached scikit_learn-1.6.1.tar.gz (7.1 MB)
  Running command pip subprocess to install build dependencies
  Using pip 25.0.1 from C:/msys64/home/oscar/projects_msys/func-ecopower-pwm-forecast-durable/.venv/lib/python3.12/site-packages/pip (python 3.12)
  Collecting meson-python>=0.16.0
    Obtaining dependency information for meson-python>=0.16.0 from https://files.pythonhosted.org/packages/7d/ec/40c0ddd29ef4daa6689a2b9c5ced47d5b58fa54ae149b19e9a97f4979c8c/meson_python-0.17.1-py3-none-any.whl.metadata
    Using cached meson_python-0.17.1-py3-none-any.whl.metadata (4.1 kB)
  Collecting Cython>=3.0.10
    Obtaining dependency information for Cython>=3.0.10 from https://files.pythonhosted.org/packages/27/6b/7c87867d255cbce8167ed99fc65635e9395d2af0f0c915428f5b17ec412d/Cython-3.0.12-py2.py3-none-any.whl.metadata
    Using cached Cython-3.0.12-py2.py3-none-any.whl.metadata (3.3 kB)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
  Collecting numpy>=2
    Using cached numpy-2.2.4-cp312-cp312-mingw_aarch64_ucrt_llvm.whl
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/99/f1/c00d6be56e1a718a3068079e3ec8ce044d7179345280f6a3f5066068af0d/scipy-1.6.2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/fe/fd/8704c7b7b34cdac850485e638346025ca57c5a859934b9aa1be5399b33b7/scipy-1.6.3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/bb/bb/944f559d554df6c9adf037aa9fc982a9706ee0e96c0d5beac701cb158900/scipy-1.7.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/47/33/a24aec22b7be7fdb10ec117a95e1e4099890d8bbc6646902f443fc7719d1/scipy-1.7.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/0e/23/58c4f995475a2a97cb5f4a032aedaf881ad87cd976a7180c55118d105a1d/scipy-1.7.2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/61/67/1a654b96309c991762ee9bc39c363fc618076b155fe52d295211cf2536c7/scipy-1.7.3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/c0/ad/e3c052ed4e0027a8abef0a5e8441a044427d252d17d9aee06d56e62fc698/scipy-1.8.0rc1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/29/d2/151a54944b333e465f98804dced31dab1284f3c37b752b9cefa710b64681/scipy-1.8.0rc2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/e4/26/83dd1c6378513a6241d984bda9f08c512b6e35fff13fba3acc1b3c195f02/scipy-1.8.0rc3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/22/78/056cc43e7737811b6f50886788a940f852773dd9804f5365952805db9648/scipy-1.8.0rc4.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/b4/a2/4faa34bf0cdbefd5c706625f1234987795f368eb4e97bde9d6f46860843e/scipy-1.8.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/26/b5/9330f004b9a3b2b6a31f59f46f1617ce9ca15c0e7fe64288c20385a05c9d/scipy-1.8.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.12'): https://files.pythonhosted.org/packages/87/82/8b9bf8bb8030f1eef281ad2af87cc648e06e4a4974c2b9201a57d991b12c/scipy-1.9.0rc1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.12)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.12'): https://files.pythonhosted.org/packages/5a/87/27f9ee75c32138d6eaabff2b91744c97a3fdbbbdd78948372dac93e0079f/scipy-1.9.0rc2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.12)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.12'): https://files.pythonhosted.org/packages/57/72/484c38e5b814b48b41ac6432ef69077f2e7c8094925d3ce17bc3d61359b0/scipy-1.9.0rc3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.12)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.12'): https://files.pythonhosted.org/packages/a8/e3/4ec401f609d34162b7023a09165da491630879e4cfa2336667fe2102cd06/scipy-1.9.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.12)
    Link requires a different Python (3.12.9 not in: '>=3.8,<3.12'): https://files.pythonhosted.org/packages/db/af/16906139f52bc6866c43401869ce247662739ad71afa11c6f18505eb0546/scipy-1.9.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.12)
    Link requires a different Python (3.12.9 not in: '<3.12,>=3.8'): https://files.pythonhosted.org/packages/a2/ce/2592c3b550cf8f68879d4ff2159f3c689ee6f032f8fc9059022074f7bd75/scipy-1.10.0rc1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:<3.12,>=3.8)
    Link requires a different Python (3.12.9 not in: '<3.12,>=3.8'): https://files.pythonhosted.org/packages/6b/a3/7de758a32569e06877a6b298bdf7b529ce97a33c55deb2b1637b0162fd9d/scipy-1.10.0rc2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:<3.12,>=3.8)
    Link requires a different Python (3.12.9 not in: '<3.12,>=3.8'): https://files.pythonhosted.org/packages/d6/bd/2d13a273d95f7b7d9903c906c486040b0aebb85e008f93a5dd0891f21f1f/scipy-1.10.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:<3.12,>=3.8)
    Link requires a different Python (3.12.9 not in: '<3.12,>=3.8'): https://files.pythonhosted.org/packages/84/a9/2bf119f3f9cff1f376f924e39cfae18dec92a1514784046d185731301281/scipy-1.10.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:<3.12,>=3.8)
  Collecting scipy>=1.6.0
    Using cached scipy-1.15.2-cp312-cp312-mingw_aarch64_ucrt_llvm.whl
  Collecting meson>=1.2.3 (from meson-python>=0.16.0)
    Obtaining dependency information for meson>=1.2.3 from https://files.pythonhosted.org/packages/ab/3b/63fdad828b4cbeb49cef3aad26f3edfbc72f37a0ab54917d445ec0b9d9ff/meson-1.7.0-py3-none-any.whl.metadata
    Using cached meson-1.7.0-py3-none-any.whl.metadata (1.8 kB)
  Collecting packaging>=19.0 (from meson-python>=0.16.0)
    Obtaining dependency information for packaging>=19.0 from https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl.metadata
    Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
  Collecting pyproject-metadata>=0.7.1 (from meson-python>=0.16.0)
    Obtaining dependency information for pyproject-metadata>=0.7.1 from https://files.pythonhosted.org/packages/7e/b1/8e63033b259e0a4e40dd1ec4a9fee17718016845048b43a36ec67d62e6fe/pyproject_metadata-0.9.1-py3-none-any.whl.metadata
    Using cached pyproject_metadata-0.9.1-py3-none-any.whl.metadata (7.0 kB)
  Using cached meson_python-0.17.1-py3-none-any.whl (27 kB)
  Using cached Cython-3.0.12-py2.py3-none-any.whl (1.2 MB)
  Using cached meson-1.7.0-py3-none-any.whl (990 kB)
  Using cached packaging-24.2-py3-none-any.whl (65 kB)
  Using cached pyproject_metadata-0.9.1-py3-none-any.whl (18 kB)
  Installing collected packages: packaging, numpy, meson, Cython, scipy, pyproject-metadata, meson-python
    Creating C:/pip_build_temp/pip-build-env-4z56ip4a/overlay/bin
  Successfully installed Cython-3.0.12 meson-1.7.0 meson-python-0.17.1 numpy-2.2.4 packaging-24.2 pyproject-metadata-0.9.1 scipy-1.15.2
  Installing build dependencies ... done
  Running command Getting requirements to build wheel
  Getting requirements to build wheel ... done
  Running command Preparing metadata (pyproject.toml)
  + meson setup C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508 C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/.mesonpy-lhh9mbac -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/.mesonpy-lhh9mbac/meson-python-native-file.ini
  The Meson build system
  Version: 1.7.0
  Source dir: C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508
  Build dir: C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/.mesonpy-lhh9mbac
  Build type: native build
  Project name: scikit-learn
  Project version: 1.6.1
  C compiler for the host machine: clang (clang 20.1.1 "clang version 20.1.1")
  C linker for the host machine: clang ld.lld 20.1.1
  C++ compiler for the host machine: clang++ (clang 20.1.1 "clang version 20.1.1")
  C++ linker for the host machine: clang++ ld.lld 20.1.1
  Cython compiler for the host machine: cython (cython 3.0.12)
  Host machine cpu family: aarch64
  Host machine cpu: aarch64
  Compiler for C supports arguments -Wno-unused-but-set-variable: YES
  Compiler for C supports arguments -Wno-unused-function: YES
  Compiler for C supports arguments -Wno-conversion: YES
  Compiler for C supports arguments -Wno-misleading-indentation: YES
  Library m found: YES
  Program python found: YES (C:/msys64/home/oscar/projects_msys/func-ecopower-pwm-forecast-durable/.venv/bin/python.exe)
  Run-time dependency OpenMP for c found: YES 5.1
  Found pkg-config: YES (C:\msys64\clangarm64\bin/pkg-config.EXE) 2.3.0
  Run-time dependency python found: YES 3.12
  Build targets in project: 111

  scikit-learn 1.6.1

    User defined options
      Native files: C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/.mesonpy-lhh9mbac/meson-python-native-file.ini
      b_ndebug    : if-release
      b_vscrt     : md
      buildtype   : release

  Found ninja.EXE-1.12.1 at C:\msys64\clangarm64\bin/ninja.EXE
  + meson compile
  [1/251] Generating sklearn/metrics/_dist_metrics_pxd with a custom command
  [2/251] Copying file sklearn/utils/_cython_blas.pxd
  [3/251] Copying file sklearn/utils/__init__.py
  [4/251] Copying file sklearn/__init__.py
  [5/251] Copying file sklearn/utils/_openmp_helpers.pxd
  [6/251] Generating sklearn/utils/_seq_dataset_pxd with a custom command
  [7/251] Copying file sklearn/utils/_sorting.pxd
  [8/251] Copying file sklearn/utils/_random.pxd
  [9/251] Generating sklearn/utils/_weight_vector_pxd with a custom command
  [10/251] Copying file sklearn/utils/_heap.pxd
  [11/251] Copying file sklearn/_loss/_loss.pxd
  [12/251] Copying file sklearn/utils/_vector_sentinel.pxd
  [13/251] Generating sklearn/metrics/_pairwise_distances_reduction/_datasets_pair_pxd with a custom command
  [14/251] Generating sklearn/metrics/_pairwise_distances_reduction/_base_pxd with a custom command
  [15/251] Generating sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_pxd with a custom command
  [16/251] Copying file sklearn/metrics/__init__.py
  [17/251] Generating sklearn/neighbors/_binary_tree_pxi with a custom command
  [18/251] Copying file sklearn/utils/_typedefs.pxd
  [19/251] Generating sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer_pxd with a custom command
  [20/251] Generating sklearn/metrics/_pairwise_distances_reduction/_argkmin_pxd with a custom command
  [21/251] Generating sklearn/_loss/_loss_pyx with a custom command
  [22/251] Copying file sklearn/metrics/_pairwise_distances_reduction/__init__.py
  [23/251] Copying file sklearn/metrics/_pairwise_distances_reduction/_classmode.pxd
  [24/251] Copying file sklearn/linear_model/__init__.py
  [25/251] Copying file sklearn/neighbors/_partition_nodes.pxd
  [26/251] Copying file sklearn/neighbors/__init__.py
  [27/251] Generating sklearn/utils/_weight_vector_pyx with a custom command
  [28/251] Generating sklearn/utils/_seq_dataset_pyx with a custom command
  [29/251] Generating sklearn/metrics/_dist_metrics_pyx with a custom command
  [30/251] Generating sklearn/metrics/_pairwise_distances_reduction/_base_pyx with a custom command
  [31/251] Generating sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer_pyx with a custom command
  [32/251] Generating sklearn/metrics/_pairwise_distances_reduction/_datasets_pair_pyx with a custom command
  [33/251] Generating sklearn/metrics/_pairwise_distances_reduction/_argkmin_pyx with a custom command
  [34/251] Generating sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_pyx with a custom command
  [35/251] Generating sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode_pyx with a custom command
  [36/251] Generating sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode_pyx with a custom command
  [37/251] Generating sklearn/linear_model/_sgd_fast_pyx with a custom command
  [38/251] Generating sklearn/neighbors/_ball_tree_pyx with a custom command
  [39/251] Generating sklearn/linear_model/_sag_fast_pyx with a custom command
  [40/251] Generating sklearn/neighbors/_kd_tree_pyx with a custom command
  [41/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/__check_build/_check_build.pyx
  [42/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_openmp_helpers.pyx
  [43/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/metrics/cluster/_expected_mutual_info_fast.pyx
  [44/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_random.pyx
  [45/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_heap.pyx
  [46/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/_isotonic.pyx
  [47/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/murmurhash.pyx
  [48/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_cython_blas.pyx
  [49/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_fast_dict.pyx
  [50/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/_sorting.pyx
  [51/251] Compiling Cython source C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508/sklearn/utils/arrayfuncs.pyx
  ninja: error: mkdir(sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cp312-mingw_aarch64_ucrt_llvm.pyd.p/sklearn/metrics/_pairwise_distances_reduction): No such file or directory
  ninja: build stopped: .
  INFO: autodetecting backend as ninja
  INFO: calculating backend command to run: C:\msys64\clangarm64\bin/ninja.EXE
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: C:/msys64/home/oscar/projects_msys/func-ecopower-pwm-forecast-durable/.venv/bin/python.exe C:/msys64/home/oscar/projects_msys/func-ecopower-pwm-forecast-durable/.venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel C:/pip_build_temp/tmpx1jq7lm1
  cwd: C:/pip_build_temp/pip-install-yjv7z3j9/scikit-learn_75cabb5c67ca4de1b01dff74d7ec4508
  Preparing metadata (pyproject.toml) ... error
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
(.venv)
oscar@pc CLANGARM64 ~/projects_msys/func-ecopower-pwm-forecast-durable
$

```
Collapsible until here.
</p></details>
**Versions**

(Cannot run `sklearn.show_versions()` as installation failed)

*   scikit-learn: 1.6.1 (attempted build from source)
*   Python: 3.12.x (mingw-w64-clang-aarch64-python)
*   OS: Windows 11 Pro 23H2 ARM64
*   Compiler: Clang 20.1.1 (mingw-w64-clang-aarch64-clang)
*   Meson: 1.7.0 (mingw-w64-clang-aarch64-meson)
*   Ninja: 1.12.1 (mingw-w64-clang-aarch64-ninja)
*   NumPy: 2.2.4 (built from source successfully in same venv)
*   SciPy: 1.15.2 (built from source successfully in same venv as build dependency)
*   MSYS2 Environment: CLANGARM64

**Possible Cause:**

The most likely cause is either hitting a path length limit within one of the build tools (Ninja?) despite OS support, or a bug in handling paths containing multiple dots or specific patterns like `.pyd.p` within the MSYS2 Clang toolchain environment on Windows ARM64.

Thanks for looking into this! Building natively on Win ARM64 is becoming increasingly relevant. I thought this was a good place to start to gather any insights on the issue.

COMMENT:
Thanks for the detailed issue 🙏! Unfortunately this will likely be a tricky one. I don't think any of the maintainers has access to a Windows ARM64 machine and even if we did, we are not super familiar with Windows compilation.

If there is a way to change our meson files without complicating it too much and to make it work for your use case, we would be willing to accept such a PR. In particular maybe there is a way to avoid such a nested folder structure `sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cp312-mingw_aarch64_ucrt_llvm.pyd.p/sklearn/metrics/_pairwise_distances_reduction`?

For the long path hypothesis, I am a bit surprised since MAXPATH is 260 characters according to this [Windows doc](https://learn.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=registry) and in the error message the path is 149 characters long but maybe this is the absolute path that counts 🤔: 

```
ninja: error: mkdir(sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cp312-mingw_aarch64_ucrt_llvm.pyd.p/sklearn/metrics/_pairwise_distances_reduction): No such file or directory
```

I did find a ninja issue https://github.com/ninja-build/ninja/issues/2442 and an ongoing PR https://github.com/ninja-build/ninja/pull/2552 that you could maybe test to see if that fixes the issue.

Labels: Build / CI, Needs Investigation, OS:Windows