Skip to content

Linux install issues #40

Description

@mdtanker

Thanks for making this package! I have been using it in Windows, but have needed to switch to Linux recently and I'm not able to install Pycurious anymore.

I'm creating a conda environment:

mamba create --name cpd numpy scipy cython python=3.7

activating it, then install pycurious with pip:

pip install pycurious

Here is the output:

Collecting pycurious
  Downloading pycurious-1.1.1.tar.gz (1.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 92.1 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (1.21.6)
Requirement already satisfied: scipy>=0.15.0 in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (1.7.3)
Requirement already satisfied: Cython>=0.25.2 in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (0.29.32)
Building wheels for collected packages: pycurious
  Building wheel for pycurious (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [73 lines of output]
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/dist.py:472: 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)
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
      !!
      
              ********************************************************************************
              Requirements should be satisfied by a PEP 517 installer.
              If you are using pip, you can try `pip install --use-pep517`.
              ********************************************************************************
      
      !!
        dist.fetch_build_eggs(dist.setup_requires)
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/dist.py:472: 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
      creating build/lib.linux-x86_64-cpython-37
      creating build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/download.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/optimise.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/grid.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/mapping.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/documentation.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/__init__.py -> build/lib.linux-x86_64-cpython-37/pycurious
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/data
      copying pycurious/Examples/data/test_mag_data.txt -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/data
      copying pycurious/Examples/0-StartHere.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex2-Compute-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex1-Plot-power-spectrum.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex3-Parameter-exploration.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex2-Compute-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex1-Plot-power-spectrum.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex4-Spatial-variation-of-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex5-Mapping-Curie-depth-EMAG2.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex3-Posing-the-inverse-problem.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      running build_ext
      building 'pycurious.radon' extension
      creating build/temp.linux-x86_64-cpython-37
      creating build/temp.linux-x86_64-cpython-37/src
      gcc -pthread -B /home/mattd/miniforge3/envs/cpd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/numpy/core/include -Isrc -I/home/mattd/miniforge3/envs/cpd/include/python3.7m -c src/cradon.c -o build/temp.linux-x86_64-cpython-37/src/cradon.o -std=c99
      error: command 'gcc' failed: No such file or directory: 'gcc'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pycurious
  Running setup.py clean for pycurious
Failed to build pycurious
ERROR: Could not build wheels for pycurious, which is required to install pyproject.toml-based projects

From this issue: #13, I also have tried installing gxx_linux-64

mamba install gxx_linux-64

And then when installing pycurious I now get the below output:

Collecting pycurious
  Downloading pycurious-1.1.1.tar.gz (1.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 88.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (1.21.6)
Requirement already satisfied: scipy>=0.15.0 in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (1.7.3)
Requirement already satisfied: Cython>=0.25.2 in /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages (from pycurious) (0.29.32)
Building wheels for collected packages: pycurious
  Building wheel for pycurious (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [79 lines of output]
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/dist.py:472: 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)
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
      !!
      
              ********************************************************************************
              Requirements should be satisfied by a PEP 517 installer.
              If you are using pip, you can try `pip install --use-pep517`.
              ********************************************************************************
      
      !!
        dist.fetch_build_eggs(dist.setup_requires)
      /home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/setuptools/dist.py:472: 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
      creating build/lib.linux-x86_64-cpython-37
      creating build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/download.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/optimise.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/grid.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/mapping.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/documentation.py -> build/lib.linux-x86_64-cpython-37/pycurious
      copying pycurious/__init__.py -> build/lib.linux-x86_64-cpython-37/pycurious
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/data
      copying pycurious/Examples/data/test_mag_data.txt -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/data
      copying pycurious/Examples/0-StartHere.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex2-Compute-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex1-Plot-power-spectrum.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      copying pycurious/Examples/Notebooks/Tanaka/Ex3-Parameter-exploration.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Tanaka
      creating build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex2-Compute-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex1-Plot-power-spectrum.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex4-Spatial-variation-of-Curie-depth.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex5-Mapping-Curie-depth-EMAG2.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      copying pycurious/Examples/Notebooks/Bouligand/Ex3-Posing-the-inverse-problem.ipynb -> build/lib.linux-x86_64-cpython-37/pycurious/Examples/Notebooks/Bouligand
      running build_ext
      building 'pycurious.radon' extension
      creating build/temp.linux-x86_64-cpython-37
      creating build/temp.linux-x86_64-cpython-37/src
      /home/mattd/miniforge3/envs/cpd/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/mattd/miniforge3/envs/cpd/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/mattd/miniforge3/envs/cpd/include -fPIC -I/home/mattd/miniforge3/envs/cpd/lib/python3.7/site-packages/numpy/core/include -Isrc -I/home/mattd/miniforge3/envs/cpd/include/python3.7m -c src/cradon.c -o build/temp.linux-x86_64-cpython-37/src/cradon.o -std=c99
      In file included from src/cradon.h:6,
                       from src/cradon.c:2:
      /home/mattd/miniforge3/envs/cpd/include/python3.7m/Python.h:44:10: fatal error: crypt.h: No such file or directory
         44 | #include <crypt.h>
            |          ^~~~~~~~~
      compilation terminated.
      error: command '/home/mattd/miniforge3/envs/cpd/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pycurious
  Running setup.py clean for pycurious
Failed to build pycurious
ERROR: Could not build wheels for pycurious, which is required to install pyproject.toml-based projects

Any suggestions for how to get PyCurious to install?

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions