lihan97 / PRS-Net

codes for PRS-Net: Interpretable polygenic risk scores via geometric learning
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Questions about installing the package #1

Open HelloWorldLTY opened 3 months ago

HelloWorldLTY commented 3 months ago

Hi, thanks for your interesting project. When installing the package to reproduce the training result, I meet an error:

      /tmp/pip-build-env-5nfkk1gy/overlay/lib/python3.7/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pyreadr.libs.lzma.lzma' is absent from the `packages` configuration.
      !!

              ********************************************************************************
              ############################
              # Package would be ignored #
              ############################
              Python recognizes 'pyreadr.libs.lzma.lzma' as an importable package[^1],
              but it is absent from setuptools' `packages` configuration.

              This leads to an ambiguous overall configuration. If you want to distribute this
              package, please make sure that 'pyreadr.libs.lzma.lzma' is explicitly added
              to the `packages` configuration field.

              Alternatively, you can also rely on setuptools' discovery methods
              (for example by using `find_namespace_packages(...)`/`find_namespace:`
              instead of `find_packages(...)`/`find:`).

              You can read more about "package discovery" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

              If you don't want 'pyreadr.libs.lzma.lzma' to be distributed and are
              already explicitly excluding 'pyreadr.libs.lzma.lzma' via
              `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
              you can try to use `exclude_package_data`, or `include-package-data=False` in
              combination with a more fine grained `package-data` configuration.

              You can read more about "package data files" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/datafiles.html

              [^1]: For Python, any directory (with suitable naming) can be imported,
                    even if it does not contain any `.py` files.
                    On the other hand, currently there is no concept of package data
                    directory, all directories are treated like packages.
              ********************************************************************************

      !!
        check.warn(importable)
      /tmp/pip-build-env-5nfkk1gy/overlay/lib/python3.7/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pyreadr.libs.zlib' is absent from the `packages` configuration.
      !!

              ********************************************************************************
              ############################
              # Package would be ignored #
              ############################
              Python recognizes 'pyreadr.libs.zlib' as an importable package[^1],
              but it is absent from setuptools' `packages` configuration.

              This leads to an ambiguous overall configuration. If you want to distribute this
              package, please make sure that 'pyreadr.libs.zlib' is explicitly added
              to the `packages` configuration field.

              Alternatively, you can also rely on setuptools' discovery methods
              (for example by using `find_namespace_packages(...)`/`find_namespace:`
              instead of `find_packages(...)`/`find:`).

              You can read more about "package discovery" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

              If you don't want 'pyreadr.libs.zlib' to be distributed and are
              already explicitly excluding 'pyreadr.libs.zlib' via
              `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
              you can try to use `exclude_package_data`, or `include-package-data=False` in
              combination with a more fine grained `package-data` configuration.

              You can read more about "package data files" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/datafiles.html

              [^1]: For Python, any directory (with suitable naming) can be imported,
                    even if it does not contain any `.py` files.
                    On the other hand, currently there is no concept of package data
                    directory, all directories are treated like packages.
              ********************************************************************************

      !!
        check.warn(importable)
      error: command '/usr/bin/gcc' 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 pyreadr
ERROR: Could not build wheels for pyreadr, which is required to install pyproject.toml-based projects

It seems that the current conda.yml file is not enough. Would you please provide more information? Thanks.

HelloWorldLTY commented 3 months ago

Also, I wonder if it is possible to directly use the example data to reproduce the baseline models, like plink, which accepts different types of data as inputs.