Skip to content
This repository was archived by the owner on Feb 15, 2023. It is now read-only.
This repository was archived by the owner on Feb 15, 2023. It is now read-only.

install openslide-python==1.1.1 error #9

Description

@PeijinV5

Hi,

How are you? I am a PhD student in Bioinformatics and Computation Medicine department at University of Michigan. I am trying to install the "requirements.txt". There was an error when trying to install open slide-python==1.1.1:

File "/tmp/pip-install-686n_fkx/openslide-python_83c86f6362ad4cd58c21cf001e9b9bb2/setup.py", line 2, in
from setuptools import setup, Extension, Feature
ImportError: cannot import name 'Feature' from 'setuptools'

I highly appreciate if you could let me know how can I fix it!

Thank you very much,
Peijin

Activity

  1. chenyang1999 commented on Jan 15, 2021

    @chenyang1999

    激活环境

    conda activate env
    

    创建指定版本 python 虚拟环境

    conda create -n env python=3.7.4
    conda activate env
    # To deactivate an active environment, use
    #
    #     $ conda deactivate
    export CUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
    python -m pip install --upgrade setuptools
    pip install --upgrade pip setuptools==45.2.0
    pip install -r requirements.txt
    
    

    安装llvmlite报错解决:RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for

    zhang@debian:~$ pip3 install llvmlite==0.16.0
    Collecting llvmlite==0.16.0
      Using cached https://files.pythonhosted.org/packages/23/c7/56d7c18564783f33206b3cb6ce861a8d681e8be1a124c5651145ce5aad0f/llvmlite-0.16.0.tar.gz
    Building wheels for collected packages: llvmlite
      Running setup.py bdist_wheel for llvmlite ... error
      Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-s7dyuobp/llvmlite/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpsklqjxv1pip-wheel- --python-tag cp35:
      running bdist_wheel
      running build
      got version from file /tmp/pip-build-s7dyuobp/llvmlite/llvmlite/_version.py {'version': '0.16.0', 'full': '964cf1d6d725b000c769379a5efe11932fcfc551'}
      running build_ext
      /usr/bin/python3 /tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py
      LLVM version... Traceback (most recent call last):
        File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 105, in main_posix
          out = subprocess.check_output([llvm_config, '--version'])
        File "/usr/lib/python3.5/subprocess.py", line 316, in check_output
          **kwargs).stdout
        File "/usr/lib/python3.5/subprocess.py", line 383, in run
          with Popen(*popenargs, **kwargs) as process:
        File "/usr/lib/python3.5/subprocess.py", line 676, in __init__
          restore_signals, start_new_session)
        File "/usr/lib/python3.5/subprocess.py", line 1282, in _execute_child
          raise child_exception_type(errno_num, err_msg)
      FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 152, in <module>
          main()
        File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 142, in main
          main_posix('linux', '.so')
        File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 108, in main_posix
          "to the path for llvm-config" % (llvm_config,))
      RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
      error: command '/usr/bin/python3' failed with exit status 1
      
      ----------------------------------------
      Failed building wheel for llvmlite
      Running setup.py clean for llvmlite
    Failed to build llvmlite
    Installing collected packages: llvmlite
      Running setup.py install for llvmlite ... error
        Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-s7dyuobp/llvmlite/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-k5q48i8w-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
        running install
        running build
        got version from file /tmp/pip-build-s7dyuobp/llvmlite/llvmlite/_version.py {'version': '0.16.0', 'full': '964cf1d6d725b000c769379a5efe11932fcfc551'}
        running build_ext
        /usr/bin/python3 /tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py
        LLVM version... Traceback (most recent call last):
          File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 105, in main_posix
            out = subprocess.check_output([llvm_config, '--version'])
          File "/usr/lib/python3.5/subprocess.py", line 316, in check_output
            **kwargs).stdout
          File "/usr/lib/python3.5/subprocess.py", line 383, in run
            with Popen(*popenargs, **kwargs) as process:
          File "/usr/lib/python3.5/subprocess.py", line 676, in __init__
            restore_signals, start_new_session)
          File "/usr/lib/python3.5/subprocess.py", line 1282, in _execute_child
            raise child_exception_type(errno_num, err_msg)
        FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
        
        During handling of the above exception, another exception occurred:
        
        Traceback (most recent call last):
          File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 152, in <module>
            main()
          File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 142, in main
            main_posix('linux', '.so')
          File "/tmp/pip-build-s7dyuobp/llvmlite/ffi/build.py", line 108, in main_posix
            "to the path for llvm-config" % (llvm_config,))
        RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
        error: command '/usr/bin/python3' failed with exit status 1
        
        ----------------------------------------
    Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-s7dyuobp/llvmlite/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-k5q48i8w-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-s7dyuobp/llvmlite/
    
    
    

    这个报错是因为找不到llvm-config这个命令:

    alias llvm-config="llvm-config-3.9"
    export LLVM_CONFIG="/usr/bin/llvm-config-3.9"
    

    然后再安装就不会报错了:

    zhang@debian:~$ pip3 install llvmlite==0.16.0
    Collecting llvmlite==0.16.0
      Using cached https://files.pythonhosted.org/packages/23/c7/56d7c18564783f33206b3cb6ce861a8d681e8be1a124c5651145ce5aad0f/llvmlite-0.16.0.tar.gz
    Building wheels for collected packages: llvmlite
      Running setup.py bdist_wheel for llvmlite ... done
      Stored in directory: /home/zhang/.cache/pip/wheels/2a/c0/a5/f0d4dc24ba9076d15b0797f84e3fc3e9a6280b56c111f0d6a2
    Successfully built llvmlite
    Installing collected packages: llvmlite
    Successfully installed llvmlite-0.16.0
    
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

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions