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ml4bio / RNA-FM

RNA foundation model
https://ml4bio.github.io/RNA-FM/
MIT License
190 stars 18 forks source link

Install Error #12

Closed Leo-T-Zang closed 2 months ago

Leo-T-Zang commented 6 months ago

Hi,

Thanks for open-sourcing this awesome work.

I met some errors when trying to install RNA-FM. Can you help me out?

Here is part of error logs.

pip install .
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Processing /workspace/work/CLIP/RNA-FM
  Preparing metadata (setup.py) ... done
Collecting numpy==1.22.0 (from rna-fm==0.1.2)
  Downloading numpy-1.22.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
Collecting pandas==1.3.1 (from rna-fm==0.1.2)
  Downloading pandas-1.3.1.tar.gz (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 11.0 MB/s eta 0:00:00
  Installing build dependencies ... error
  error: subprocess-exited-with-error

  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [824 lines of output]
      Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com, https://pypi.ngc.nvidia.com
      Ignoring numpy: markers 'python_version == "3.7" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_machine != "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_machine != "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.7" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.9" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment
      Collecting setuptools>=38.6.0
        Downloading setuptools-69.1.1-py3-none-any.whl.metadata (6.2 kB)
      Collecting wheel
        Downloading wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
      Collecting Cython<3,>=0.29.21
        Downloading Cython-0.29.37-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.1 kB)
      Collecting numpy==1.19.3
        Downloading numpy-1.19.3.zip (7.3 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 11.3 MB/s eta 0:00:00
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Downloading setuptools-69.1.1-py3-none-any.whl (819 kB)
         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.3/819.3 kB 11.8 MB/s eta 0:00:00
      Downloading wheel-0.43.0-py3-none-any.whl (65 kB)
         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 13.1 MB/s eta 0:00:00
      Downloading Cython-0.29.37-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 11.8 MB/s eta 0:00:00
      Building wheels for collected packages: numpy
        Building wheel for numpy (pyproject.toml): started
        Building wheel for numpy (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error

        × Building wheel for numpy (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [782 lines of output]
            setup.py:67: RuntimeWarning: NumPy 1.19.3 may not yet support Python 3.10.
              warnings.warn(
            Running from numpy source directory.
            /tmp/pip-install-9x5z1ps4/numpy_11ee67fb2b2142c4bcbc63b744069658/tools/cythonize.py:67: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
              from distutils.version import LooseVersion
            numpy/random/_bounded_integers.pxd.in has not changed
            numpy/random/_pcg64.pyx has not changed
            numpy/random/_philox.pyx has not changed
            numpy/random/bit_generator.pyx has not changed
            numpy/random/_common.pyx has not changed
            numpy/random/_bounded_integers.pyx.in has not changed
            numpy/random/mtrand.pyx has not changed
            numpy/random/_mt19937.pyx has not changed
            numpy/random/_sfc64.pyx has not changed
            numpy/random/_generator.pyx has not changed
            Processing numpy/random/_bounded_integers.pyx
            Cythonizing sources
            blas_opt_info:
            blas_mkl_info:
            customize UnixCCompiler
              FOUND:
                libraries = ['mkl_rt', 'pthread']
                library_dirs = ['/usr/local/lib']
                define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
                include_dirs = ['/usr/local/include', '/usr/include']

              FOUND:
                libraries = ['mkl_rt', 'pthread']
                library_dirs = ['/usr/local/lib']
                define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
                include_dirs = ['/usr/local/include', '/usr/include']

            non-existing path in 'numpy/distutils': 'site.cfg'
            lapack_opt_info:
            lapack_mkl_info:
              FOUND:
                libraries = ['mkl_rt', 'pthread']
                library_dirs = ['/usr/local/lib']
                define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
                include_dirs = ['/usr/local/include', '/usr/include']

              FOUND:
                libraries = ['mkl_rt', 'pthread']
                library_dirs = ['/usr/local/lib']
                define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
                include_dirs = ['/usr/local/include', '/usr/include']

            /usr/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
              warnings.warn(msg)
            running bdist_wheel
            running build
            running config_cc
            unifing config_cc, config, build_clib, build_ext, build commands --compiler options
            running config_fc
            unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
            running build_src
            build_src
            building py_modules sources
            building library "npymath" sources
              adding 'build/src.linux-x86_64-3.10/numpy/core/src/npymath' to include_dirs.
            None - nothing done with h_files = ['build/src.linux-x86_64-3.10/numpy/core/src/npymath/npy_math_internal.h']
            building library "npysort" sources
              adding 'build/src.linux-x86_64-3.10/numpy/core/src/common' to include_dirs.
            None - nothing done with h_files = ['build/src.linux-x86_64-3.10/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.10/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.10/numpy/core/src/common/npy_binsearch.h']
            building library "npyrandom" sources
            building extension "numpy.core._multiarray_tests" sources
            building extension "numpy.core._multiarray_umath" sources
              adding 'build/src.linux-x86_64-3.10/numpy/core/src/umath' to include_dirs.
              adding 'build/src.linux-x86_64-3.10/numpy/core/src/npymath' to include_dirs.
              adding 'build/src.linux-x86_64-3.10/numpy/core/src/common' to include_dirs.
            numpy.core - nothing done with h_files = ['build/src.linux-x86_64-3.10/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-3.10/numpy/core/src/umath/simd.inc', 'build/src.linux-x86_64-3.10/numpy/core/src/umath/loops.h', 'build/src.linux-x86_64-3.10/numpy/core/src/umath/matmul.h', 'build/src.linux-x86_64-3.10/numpy/core/src/umath/clip.h', 'build/src.linux-x86_64-3.10/numpy/core/src/npymath/npy_math_internal.h', 'build/src.linux-x86_64-3.10/numpy/core/src/common/templ_common.h', 'build/src.linux-x86_64-3.10/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-3.10/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-3.10/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-3.10/numpy/core/include/numpy/__ufunc_api.h']
Leo-T-Zang commented 6 months ago

If I use pip install rna-fm or git clone + pip, I will encounter same error. I fix this by creating a conda env as you put in the instruction and then use pip to install. Maybe you can look into this problem

mydkzgj commented 6 months ago

Hi, maybe you can try to reinstall RNA-FM through the 'pip' command right now, I have made some revisions regarding the dependencies of the package.