无法使用conda install或pip安装scanpy包

Question

我一直在尝试在anaconda中安装scanpy包，使用

conda install scanpy

对于一些不可满足的错误，它不起作用。然后我试着用

pip install scanpy

它给了我一个关于llvmlite的错误，我也安装了llvmlite，但它仍然不能工作。它显示了下面的错误。

    Building wheel for llvmlite (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /media/asif/LocalDisc1/anaconda3/envs/scRNAseq/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/setup.py'"'"'; __file__='"'"'/tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/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/pip-wheel-kgjl38x2
       cwd: /tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/
  Complete output (26 lines):
  running bdist_wheel
  /media/asif/LocalDisc1/anaconda3/envs/scRNAseq/bin/python3.9 /tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/ffi/build.py
  LLVM version... Traceback (most recent call last):
    File "/tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/ffi/build.py", line 105, in main_posix
      out = subprocess.check_output([llvm_config, '--version'])
    File "/media/asif/LocalDisc1/anaconda3/envs/scRNAseq/lib/python3.9/subprocess.py", line 420, in check_output
      return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
    File "/media/asif/LocalDisc1/anaconda3/envs/scRNAseq/lib/python3.9/subprocess.py", line 501, in run
      with Popen(*popenargs, **kwargs) as process:
    File "/media/asif/LocalDisc1/anaconda3/envs/scRNAseq/lib/python3.9/subprocess.py", line 947, in __init__
      self._execute_child(args, executable, preexec_fn, close_fds,
    File "/media/asif/LocalDisc1/anaconda3/envs/scRNAseq/lib/python3.9/subprocess.py", line 1819, in _execute_child
      raise child_exception_type(errno_num, err_msg, err_filename)
  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-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/ffi/build.py", line 191, in <module>
      main()
    File "/tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/ffi/build.py", line 181, in main
      main_posix('linux', '.so')
    File "/tmp/pip-install-jau3fq4a/llvmlite_c960ef5cb4c84cd089c0efb72aecc497/ffi/build.py", line 107, in main_posix
      raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
  RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
  error: command '/media/asif/LocalDisc1/anaconda3/envs/scRNAseq/bin/python3.9' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for llvmlite

Answer 1

在错误日志中，您可以看到

please point LLVM_CONFIG to the path for llvm-config

这可能意味着您必须在~/.bashrc中设置LLVM_CONFIG，如下所示

export LLVM_CONFIG=/usr/local/opt/llvm@9/bin/llvm-config

做完这件事后，记得把它找出来。

source ~/.bashrc or . ~/.bashrc