Unable to install pyradiomics for python 3.11

[sarthakpati]

@JoostJM is this issue done? I am seeing this on the latest 3.1.0 release as well (on both Windows and Linux systems):

$> pip install pyradiomics==3.1.0
Using Python 3.11.13 environment at: venv
Resolved 10 packages in 29ms
  × Failed to build `pyradiomics==3.1.0`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1)

      [stdout]
      Failed to load config from /hm/sp/.cache/uv/sdists-v9/pypi/pyradiomics/3.1.0/ElkUNvx-H6Fm-s9qjePzt/src/pyproject.toml: 'tool'
      Try to load it from setup.cfg
      running bdist_wheel
      running build
      running build_py
      Failed to load config from /hm/sp/.cache/uv/sdists-v9/pypi/pyradiomics/3.1.0/ElkUNvx-H6Fm-s9qjePzt/src/pyproject.toml: 'tool'
      Try to load it from setup.cfg
      Failed to load config from /hm/sp/.cache/uv/sdists-v9/pypi/pyradiomics/3.1.0/ElkUNvx-H6Fm-s9qjePzt/src/pyproject.toml: 'tool'
      Try to load it from setup.cfg
      copying radiomics/glszm.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/generalinfo.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/shape.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/featureextractor.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/gldm.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/shape2D.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/ngtdm.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/glcm.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/base.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/glrlm.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/imageoperations.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/__init__.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/firstorder.py -> build/lib.linux-x86_64-cpython-311/radiomics
      copying radiomics/scripts/segment.py -> build/lib.linux-x86_64-cpython-311/radiomics/scripts
      copying radiomics/scripts/voxel.py -> build/lib.linux-x86_64-cpython-311/radiomics/scripts
      copying radiomics/scripts/__init__.py -> build/lib.linux-x86_64-cpython-311/radiomics/scripts
      copying radiomics/schemas/paramSchema.yaml -> build/lib.linux-x86_64-cpython-311/radiomics/schemas
      copying radiomics/schemas/schemaFuncs.py -> build/lib.linux-x86_64-cpython-311/radiomics/schemas
      UPDATING build/lib.linux-x86_64-cpython-311/radiomics/_version.py
      set build/lib.linux-x86_64-cpython-311/radiomics/_version.py to 'v3.1.0'
      running build_ext
      Failed to load config from /hm/sp/.cache/uv/sdists-v9/pypi/pyradiomics/3.1.0/ElkUNvx-H6Fm-s9qjePzt/src/pyproject.toml: 'tool'
      Try to load it from setup.cfg
      Failed to load config from /hm/sp/.cache/uv/sdists-v9/pypi/pyradiomics/3.1.0/ElkUNvx-H6Fm-s9qjePzt/src/pyproject.toml: 'tool'
      Try to load it from setup.cfg
      building 'radiomics._cmatrices' extension
      gcc -pthread -B /hm/sp/proj/venv/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /hm/sp/proj/venv/include
      -fPIC -O2 -isystem /hm/sp/proj/venv/include -fPIC -I/hm/sp/proj/venv/include/python3.11
      -I/hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/numpy/_core/include -I/hm/sp/.cache/uv/builds-v0/.tmprzIeg3/include
      -I/hm/sp/proj/venv/include/python3.11 -c radiomics/src/_cmatrices.c -o build/temp.linux-x86_64-cpython-311/radiomics/src/_cmatrices.o

      [stderr]
      /hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/setuptools/dist.py:332: InformationOnly: Normalizing 'v3.1.0' to '3.1.0'
        self.metadata.version = self._normalize_version(self.metadata.version)
      /hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
      !!

              ********************************************************************************
              Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

              By 2026-Feb-18, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        corresp(dist, value, root_dir)
      /hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml`
      (dependencies)
        corresp(dist, value, root_dir)
      /hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!

              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:

              License :: OSI Approved :: BSD License

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        dist._finalize_license_expression()
      /hm/sp/.cache/uv/builds-v0/.tmprzIeg3/lib/python3.11/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!

              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:

              License :: OSI Approved :: BSD License

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        self._finalize_license_expression()
      radiomics/src/_cmatrices.c:6:10: fatal error: cmatrices.h: No such file or directory
          6 | #include "cmatrices.h"
            |          ^~~~~~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1

      hint: This error likely indicates that you need to install a library that provides "cmatrices.h" for `pyradiomics@3.0.1a1`

Originally posted by @sarthakpati in #829

This was using python-3.11. I have tried installing pyradiomics using a fresh environment for python-3.10, with different errors:

(C:\Projects\radiomics\venv) PS C:\Projects\radiomics> conda create -p ./venv310 python=3.10 -y
Channels:
 - defaults
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
    current version: 25.1.1
    latest version: 25.5.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Projects\radiomics\venv310

  added / updated specs:
    - python=3.10


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-3.10.18             |       h981015d_0        16.2 MB
    setuptools-78.1.1          |  py310haa95532_0         1.7 MB
    wheel-0.45.1               |  py310haa95532_0         145 KB
    ------------------------------------------------------------
                                           Total:        18.0 MB

The following NEW packages will be INSTALLED:

  bzip2              pkgs/main/win-64::bzip2-1.0.8-h2bbff1b_6
  ca-certificates    pkgs/main/win-64::ca-certificates-2025.2.25-haa95532_0
  expat              pkgs/main/win-64::expat-2.7.1-h8ddb27b_0
  libffi             pkgs/main/win-64::libffi-3.4.4-hd77b12b_1
  openssl            pkgs/main/win-64::openssl-3.0.16-h3f729d1_0
  pip                pkgs/main/noarch::pip-25.1-pyhc872135_2
  python             pkgs/main/win-64::python-3.10.18-h981015d_0
  setuptools         pkgs/main/win-64::setuptools-78.1.1-py310haa95532_0
  sqlite             pkgs/main/win-64::sqlite-3.50.2-hda9a48d_0
  tk                 pkgs/main/win-64::tk-8.6.14-h5e9d12e_1
  tzdata             pkgs/main/noarch::tzdata-2025b-h04d1e81_0
  ucrt               pkgs/main/win-64::ucrt-10.0.22621.0-haa95532_0
  vc                 pkgs/main/win-64::vc-14.3-h2df5915_10
  vc14_runtime       pkgs/main/win-64::vc14_runtime-14.44.35208-h4927774_10
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.44.35208-ha6b5a95_10
  wheel              pkgs/main/win-64::wheel-0.45.1-py310haa95532_0
  xz                 pkgs/main/win-64::xz-5.6.4-h4754444_1
  zlib               pkgs/main/win-64::zlib-1.2.13-h8cc25b3_1



Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate C:\Projects\radiomics\venv310
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(C:\Projects\radiomics\venv) PS C:\Projects\radiomics> conda activate ./venv310
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> pip install pyradiomics==3.1.0
Collecting pyradiomics==3.1.0
  Downloading pyradiomics-3.1.0.tar.gz (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 33.2 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  WARNING: Requested pyradiomics==3.1.0 from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz, but installing version 3.0.1a1
Discarding https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz (from https://pypi.org/simple/pyradiomics/): Requested pyradiomics==3.1.0 from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'
ERROR: Could not find a version that satisfies the requirement pyradiomics==3.1.0 (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 3.0, 3.0.1a3, 3.0.1, 3.1.0)
ERROR: No matching distribution found for pyradiomics==3.1.0
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> pip install pyradiomics==3^C
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics>  & 'c:\Projects\PyRanker\venv\python.exe' 'c:\Users\sarth\.vscode\extensions\ms-python.debugpy-2025.10.0-win32-x64\bundled\libs\debugpy\launcher' '60067' '--' 'C:\Projects\PyRanker\pyranker\cli\run.py' './data/' './data/output_6' ^C
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> ^C
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> pip install pyradiomics==3.0.1
Collecting pyradiomics==3.0.1
  Downloading pyradiomics-3.0.1.tar.gz (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 33.7 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 35, in <module>
        File "C:\Users\sarth\AppData\Local\Temp\pip-install-3se_z5cn\pyradiomics_80042bfca92c43449d22217cb2c4884a\setup.py", line 7, in <module>
          import numpy
      ModuleNotFoundError: No module named 'numpy'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
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.
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> pip install pyradiomics==3.0
Collecting pyradiomics==3.0
  Downloading pyradiomics-3.0.tar.gz (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 30.0 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 35, in <module>
        File "C:\Users\sarth\AppData\Local\Temp\pip-install-lp8cju04\pyradiomics_5d9b47641abb4a468f06cca33202ce11\setup.py", line 7, in <module>
          import numpy
      ModuleNotFoundError: No module named 'numpy'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
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.
(C:\Projects\radiomics\venv310) PS C:\Projects\radiomics> pip install pyradiomics==3.1
Collecting pyradiomics==3.1
  Using cached pyradiomics-3.1.0.tar.gz (34.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  WARNING: Requested pyradiomics==3.1 from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz, but installing version 3.0.1a1
Discarding https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz (from https://pypi.org/simple/pyradiomics/): Requested pyradiomics==3.1 from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'
ERROR: Could not find a version that satisfies the requirement pyradiomics==3.1 (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 3.0, 3.0.1a3, 3.0.1, 3.1.0)
ERROR: No matching distribution found for pyradiomics==3.1

Here's some debugging information for you:

Platform: Windows-10-10.0.26100-SP0
Machine: AMD64
Processor: Intel64 Family 6 Model 165 Stepping 2, GenuineIntel
Architecture: 64bit WindowsPE

Let me know what else you'd need.

[xinyiwan]

For the second error, you could try to install numpy first before install predict.

[sarthakpati]

Already tried installing numpy first, and it didn't work.

[xinyiwan]

Emm. I just made a clean enviroment (python 3.11.3), and installed numpy + scipy before installing pyradiomics. And it worked. Maybe try both? Though I don't see the reasoning.
It first tried to install Pyradiomics 3.1.0, but this version seemed to be discarded, instead it installed pyradiomics-3.0.1 smoothly.

[sarthakpati]

I just made a clean enviroment (python 3.11.3), and installed numpy + scipy before installing pyradiomics. And it worked.

That is so weird. I tried the same thing and it also worked for both 3.10 and 3.11.

Is this some issue with the way pyradiomics is getting packaged?

[k-bose]

Try installing "numpy<2.0"

$ pip install "numpy<2.0"
$ pip install versioneer setuptools
$ pip install pyradiomics

[gregspangenberg]

I had this same issue and it wasn't resolved by installing numpy lower than 2.0, or any of the above suggestions. What worked for me was using the --nobuild-isolation flag when installing:
pip install pyradiomics --no-build-isolation

[sarthakpati]

Very interesting. This usually means that the user's system packages are interfering with the installation (which could also be why I was seeing those issues). I am curious what the maintainers have to say, though.

[eliopato]

I had the same issue trying to install pyradiomics (3.1.0 or 3.0.1) with python 3.12, but the suggested solutions above didn't work. I finally managed to get it to run by installing it with pip install git+https://github.com/AIM-Harvard/pyradiomics@v3.1.0
if it can be useful to anyone struggling like me :)

[So-cean]

I had the same issue trying to install pyradiomics (3.1.0 or 3.0.1) with python 3.12, but the suggested solutions above didn't work. I finally managed to get it to run by installing it with if it can be useful to anyone struggling like me :)pip install git+https://github.com/AIM-Harvard/pyradiomics@v3.1.0
really work for python3.12 on Windwos