[INSTALLATION ERROR] : Failed building wheel for python-pysap

[albanPi]

System setup
OS: Ubuntu 22.04.5 LTS
Python version: 3.11.11
Python environment : conda 23.5.0

Describe the bug
When installing Pysap an error raise with the message : ERROR: Failed building wheel for python-pysap and then ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (python-pysap).

To Reproduce
pip install python-pysap in conda env.

Error message

Collecting python-pysap
  Using cached python-PySAP-0.2.1.tar.gz (52 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: scipy>=1.5.4 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (1.14.1)
Requirement already satisfied: numpy>=1.19.5 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (1.24.3)
Requirement already satisfied: matplotlib>=3.3.4 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (3.9.2)
Requirement already satisfied: astropy>=4.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (7.0.0)
Requirement already satisfied: nibabel>=3.2.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (5.3.2)
Requirement already satisfied: progressbar2>=3.53.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (4.5.0)
Requirement already satisfied: modopt>=1.6.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (1.7.2)
Requirement already satisfied: scikit-learn>=0.24.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (1.5.2)
Collecting scikit-image>=0.17.2 (from python-pysap)
  Downloading scikit_image-0.25.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
Requirement already satisfied: PyWavelets>=1.1.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-pysap) (1.8.0)
Requirement already satisfied: pyerfa>=2.0.1.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from astropy>=4.1->python-pysap) (2.0.1.5)
Requirement already satisfied: astropy-iers-data>=0.2024.10.28.0.34.7 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from astropy>=4.1->python-pysap) (0.2024.12.30.0.33.36)
Requirement already satisfied: PyYAML>=6.0.0 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from astropy>=4.1->python-pysap) (6.0.2)
Requirement already satisfied: packaging>=22.0.0 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from astropy>=4.1->python-pysap) (23.1)
Requirement already satisfied: contourpy>=1.0.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (1.0.7)
Requirement already satisfied: cycler>=0.10 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (4.39.4)
Requirement already satisfied: kiwisolver>=1.3.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (1.4.4)
Requirement already satisfied: pillow>=8 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (11.0.0)
Requirement already satisfied: pyparsing>=2.3.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (3.2.0)
Requirement already satisfied: python-dateutil>=2.7 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from matplotlib>=3.3.4->python-pysap) (2.9.0.post0)
Requirement already satisfied: tqdm in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from modopt>=1.6.1->python-pysap) (4.66.5)
Requirement already satisfied: importlib-metadata in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from modopt>=1.6.1->python-pysap) (8.5.0)
Requirement already satisfied: importlib-resources>=5.12 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from nibabel>=3.2.1->python-pysap) (6.5.2)
Requirement already satisfied: typing-extensions>=4.6 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from nibabel>=3.2.1->python-pysap) (4.12.2)
Requirement already satisfied: python-utils>=3.8.1 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from progressbar2>=3.53.1->python-pysap) (3.9.1)
Collecting networkx>=3.0 (from scikit-image>=0.17.2->python-pysap)
  Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.17.2->python-pysap)
  Downloading imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
Collecting tifffile>=2022.8.12 (from scikit-image>=0.17.2->python-pysap)
  Downloading tifffile-2025.1.10-py3-none-any.whl.metadata (31 kB)
Collecting lazy-loader>=0.4 (from scikit-image>=0.17.2->python-pysap)
  Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Requirement already satisfied: joblib>=1.2.0 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from scikit-learn>=0.24.1->python-pysap) (1.4.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from scikit-learn>=0.24.1->python-pysap) (3.5.0)
Requirement already satisfied: six>=1.5 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib>=3.3.4->python-pysap) (1.16.0)
Requirement already satisfied: zipp>=3.20 in /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages (from importlib-metadata->modopt>=1.6.1->python-pysap) (3.21.0)
Downloading scikit_image-0.25.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.8/14.8 MB 3.8 MB/s eta 0:00:00
Downloading imageio-2.37.0-py3-none-any.whl (315 kB)
Using cached lazy_loader-0.4-py3-none-any.whl (12 kB)
Using cached networkx-3.4.2-py3-none-any.whl (1.7 MB)
Downloading tifffile-2025.1.10-py3-none-any.whl (227 kB)
Building wheels for collected packages: python-pysap
  Building wheel for python-pysap (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [812 lines of output]
      /tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/setup.py:22: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
      !!
      
              ********************************************************************************
              Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
      
              This deprecation is overdue, please update your project and remove deprecated
              calls to avoid build errors in the future.
              ********************************************************************************
      
      !!
        from setuptools.command.test import test as TestCommand
      /home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!
      
              ********************************************************************************
              Usage of dash-separated 'description-file' will not be supported in future
              versions. Please use the underscore name 'description_file' instead.
      
              This deprecation is overdue, please update your project and remove deprecated
              calls to avoid build errors in the future.
      
              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************
      
      !!
        opt = self.warn_dash_deprecation(opt, section)
      running bdist_wheel
      running build
      running build_py
      creating build/lib.linux-x86_64-cpython-311/pysap
      copying pysap/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap
      copying pysap/data.py -> build/lib.linux-x86_64-cpython-311/pysap
      copying pysap/info.py -> build/lib.linux-x86_64-cpython-311/pysap
      copying pysap/utils.py -> build/lib.linux-x86_64-cpython-311/pysap
      copying pysap/configure.py -> build/lib.linux-x86_64-cpython-311/pysap
      creating build/lib.linux-x86_64-cpython-311/pysap/plugins
      copying pysap/plugins/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/plugins
      creating build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/sparse2d.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/formating.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/tools.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/wrapper.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      copying pysap/extensions/transform.py -> build/lib.linux-x86_64-cpython-311/pysap/extensions
      creating build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/image.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/observable.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/utils.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/exceptions.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/io.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/plugins.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      copying pysap/base/transform.py -> build/lib.linux-x86_64-cpython-311/pysap/base
      creating build/lib.linux-x86_64-cpython-311/pysap/plotting
      copying pysap/plotting/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/plotting
      copying pysap/plotting/image.py -> build/lib.linux-x86_64-cpython-311/pysap/plotting
      copying pysap/plotting/utils.py -> build/lib.linux-x86_64-cpython-311/pysap/plotting
      copying pysap/plotting/transform.py -> build/lib.linux-x86_64-cpython-311/pysap/plotting
      creating build/lib.linux-x86_64-cpython-311/pysap/apps
      copying pysap/apps/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/apps
      creating build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/loader_base.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/nifti.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/__init__.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/numpy_binary.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/fits.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/mat.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      copying pysap/base/loaders/tif.py -> build/lib.linux-x86_64-cpython-311/pysap/base/loaders
      creating build/lib.linux-x86_64-cpython-311/pysap/test
      copying pysap/test/test_examples.py -> build/lib.linux-x86_64-cpython-311/pysap/test
      copying pysap/test/test_binding.py -> build/lib.linux-x86_64-cpython-311/pysap/test
      copying pysap/test/errors.json -> build/lib.linux-x86_64-cpython-311/pysap/test
      copying pysap/apps/pypipe_config.json -> build/lib.linux-x86_64-cpython-311/pysap/apps
      running build_ext
      /tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/setup.py:97: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
        cmake_version = LooseVersion(
      Building "pysparse" in build/temp.linux-x86_64-cpython-311...
      Cmake args:
      ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/lib.linux-x86_64-cpython-311',
       '-DPYTHON_EXECUTABLE=/home/albqn/anaconda3/envs/benchopt/bin/python',
       '-DCMAKE_BUILD_TYPE=Release']
      Cmake build args:
      ['--config', 'Release', '--', '-j8']
      -- The C compiler identification is GNU 11.4.0
      -- The CXX compiler identification is GNU 11.4.0
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Check for working C compiler: /usr/bin/cc - skipped
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /usr/bin/c++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Binary output path : /home/albqn/anaconda3/envs/benchopt/bin
      -- Configuring done
      -- Generating done
      -- Build files have been written to: /tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311
      [ 12%] Creating directories for 'sparse2d'
      [ 25%] Performing download step (git clone) for 'sparse2d'
      Cloning into 'sparse2d'...
      Already on 'master'
      Your branch is up to date with 'origin/master'.
      [ 37%] Performing update step for 'sparse2d'
      HEAD is now at 9d03f0f Inpaint gmca (#54)
      [ 50%] No patch step for 'sparse2d'
      [ 62%] Performing configure step for 'sparse2d'
      -- The CXX compiler identification is GNU 11.4.0
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /usr/bin/c++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
      -- CMake Build Type: RELEASE
      -- Found Python: /home/albqn/anaconda3/envs/benchopt/bin/python3.1 (found version "3.11.11") found components: Interpreter Development Development.Module Development.Embed
      -- pybind11 v2.10.3
      -- Performing Test HAS_FLTO
      -- Performing Test HAS_FLTO - Success
      -- Found OpenMP_CXX: -fopenmp (found version "4.5")
      -- Found OpenMP: TRUE (found version "4.5")
      CMake Warning at CMakeLists.txt:82 (find_package):
        By not providing "FindCatch2.cmake" in CMAKE_MODULE_PATH this project has
        asked CMake to find a package configuration file provided by "Catch2", but
        CMake did not find one.
      
        Could not find a package configuration file provided by "Catch2" (requested
        version 3) with any of the following names:
      
          Catch2Config.cmake
          catch2-config.cmake
      
        Add the installation prefix of "Catch2" to CMAKE_PREFIX_PATH or set
        "Catch2_DIR" to a directory containing one of the above files.  If "Catch2"
        provides a separate development package or SDK, be sure it has been
        installed.
      
      
      -- CFITSIO will be built from source.
      -- Configuring done
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target cur_contrast because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target cur_deconv because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target cur_filter because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target cur_stat because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target cur_trans because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_convert because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_der_loggamma
        because files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_info because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_period because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_stf because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_tend because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target im1d_tfreq because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr1d_detect because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr1d_filter because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr1d_trans because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr2d1d_stat because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr2d1d_trans because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr3d_filter because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr3d_recons because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr3d_stat because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr3d_trans because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_deconv because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_filter because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_info because files
        in some directories may conflict with libraries in implicit directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_recons because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_transform because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPackage.cmake:79 (add_executable):
        Cannot generate a safe runtime search path for target mr_ulc_filter because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPackage.cmake:95 (build_bin)
        cmake/BuildPackage.cmake:107 (build_bin_list)
        cmake/BuildPackage.cmake:30 (build_main_list)
        src/CMakeLists.txt:30 (build_package)
      
      
      CMake Warning at cmake/BuildPybind.cmake:39 (add_library):
        Cannot generate a safe runtime search path for target pysparse because
        files in some directories may conflict with libraries in implicit
        directories:
      
          runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
            /home/albqn/anaconda3/envs/benchopt/lib
      
        Some of these libraries may not be found correctly.
      Call Stack (most recent call first):
        cmake/BuildPybind.cmake:27 (build_pybind_target)
        src/CMakeLists.txt:251 (build_pybind)
      
      
      -- Generating done
      -- Build files have been written to: /tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311/sparse2d/src/sparse2d-build
      [ 75%] Performing build step for 'sparse2d'
      make[3]: warning: -j8 forced in submake: resetting jobserver mode.
      [  0%] Creating directories for 'cfitsio_build'
      [  0%] Performing download step (download, verify and extract) for 'cfitsio_build'
      -- Downloading...
         dst='/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311/sparse2d/src/sparse2d-build/cfitsio/src/cfitsio-4.1.0.tar.gz'
         timeout='none'
         inactivity timeout='none'
      -- Using src='http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-4.1.0.tar.gz'
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      -- verifying file...
             file='/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311/sparse2d/src/sparse2d-build/cfitsio/src/cfitsio-4.1.0.tar.gz'
      -- Downloading... done
      -- extracting...
           src='/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311/sparse2d/src/sparse2d-build/cfitsio/src/cfitsio-4.1.0.tar.gz'
           dst='/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/build/temp.linux-x86_64-cpython-311/sparse2d/src/sparse2d-build/cfitsio/src/cfitsio_build'
      -- extracting... [tar xfz]
      -- extracting... [analysis]
      -- extracting... [rename]
      -- extracting... [clean up]
      -- extracting... done
      [  0%] No update step for 'cfitsio_build'
      [  1%] No patch step for 'cfitsio_build'
      [  2%] Performing configure step for 'cfitsio_build'
      checking build system type... x86_64-pc-linux-gnu
      checking host system type... x86_64-pc-linux-gnu
      checking target system type... x86_64-pc-linux-gnu
      checking for gcc... gcc
      checking whether the C compiler works... yes
      checking for C compiler default output file name... a.out
      checking for suffix of executables...
      checking whether we are cross compiling... no
      checking for suffix of object files... o
      checking whether the compiler supports GNU C... yes
      checking whether gcc accepts -g... yes
      checking for gcc option to enable C11 features... none needed
      checking for stdio.h... yes
      checking for stdlib.h... yes
      checking for string.h... yes
      checking for inttypes.h... yes
      checking for stdint.h... yes
      checking for strings.h... yes
      checking for sys/stat.h... yes
      checking for sys/types.h... yes
      checking for unistd.h... yes
      checking for gcc... (cached) gcc
      checking whether the compiler supports GNU C... (cached) yes
      checking whether gcc accepts -g... (cached) yes
      checking for gcc option to enable C11 features... (cached) none needed
      checking for gfortran... no
      checking for g95... no
      checking for g77... no
      checking for f77... no
      checking for ifort... no
      checking for f95... no
      checking for f90... no
      checking for xlf... no
      checking for cf77... no
      checking for gf77... no
      checking for af77... no
      checking for ncf... no
      checking for f2c... no
      configure: WARNING: cfitsio: == No acceptable Fortran compiler found in $PATH
      configure: cfitsio: == Adding wrapper support for GNU Fortran by default
      checking for ar... ar
      checking for ranlib... ranlib
      checking for stdlib.h... (cached) yes
      checking for string.h... (cached) yes
      checking for math.h... yes
      checking for limits.h... yes
      cfitsio: == Using gcc version 11
      checking for curl-config... no
      configure: WARNING: curl-config not found. Disabling curl support.
      checking for inflateEnd in -lz... no
      configure: error: Unable to locate zlib compression library
      make[5]: *** [CMakeFiles/cfitsio_build.dir/build.make:92: cfitsio/src/cfitsio_build-stamp/cfitsio_build-configure] Error 1
      make[4]: *** [CMakeFiles/Makefile2:182: CMakeFiles/cfitsio_build.dir/all] Error 2
      make[3]: *** [Makefile:136: all] Error 2
      gmake[2]: *** [CMakeFiles/sparse2d.dir/build.make:86: sparse2d/src/sparse2d-stamp/sparse2d-build] Error 2
      gmake[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/sparse2d.dir/all] Error 2
      gmake: *** [Makefile:91: all] Error 2
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/setup.py", line 204, in <module>
          setup(
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 183, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
          dist.run_commands()
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
          self.run_command(cmd)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/dist.py", line 950, in run_command
          super().run_command(command)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/command/bdist_wheel.py", line 398, in run
          self.run_command("build")
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
          self.distribution.run_command(command)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/dist.py", line 950, in run_command
          super().run_command(command)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
          self.distribution.run_command(command)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/dist.py", line 950, in run_command
          super().run_command(command)
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/setup.py", line 105, in run
          self.build_extension(ext)
        File "/tmp/pip-install-l_bir903/python-pysap_93c140322e6240a68dfc5b7ca0dfcb2f/setup.py", line 151, in build_extension
          subprocess.check_call(
        File "/home/albqn/anaconda3/envs/benchopt/lib/python3.11/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j8']' returned non-zero exit status 2.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for python-pysap
  Running setup.py clean for python-pysap
Failed to build python-pysap
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (python-pysap)

Are you planning to submit a Pull Request?

• Yes
• No

[sfarrens]

Hi @albanPi , thanks for raising the issue. I will try to investigate as soon as I can find some time.