无法安装autodock vina(可能是由于boost)

问题描述 投票:0回答:1

作为我正在编写的脚本的一部分,我需要安装 autodock vina 软件包以实现配体和蛋白质结合。每次我尝试“pip install vina”时,都会收到一条错误消息“ValueError:未找到 Boost 库位置!”。在尝试手动安装 boost 时,我无法运行引导程序文件,因为它没有创建在线教程所说的 b2 文件夹。

为了解决这个问题,我安装了 conda,并创建了一个包含所有先决条件(包括 boost)的活动环境。我已经检查了所有这些先决条件的版本并确认了它们的存在,并仔细检查了我是否处于写入活动环境中。安装后,我要么遇到同样的问题(使用 conda install vina),要么在使用“conda install -c bioconda autodock-vina”时,收到一条消息说该包不存在(尽管添加了 cforge 和 bioconda 作为活动包处理程序) ,并且该包的存在在网上有明确记录)。有没有人有什么建议?我已经尝试安装这个软件 3 天了,我已经完全用尽了文档以及所有其他类似问题的答案,但没有任何效果。

完整错误消息:

Collecting vina
  Using cached vina-1.2.3.tar.gz (95 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [56 lines of output]
      Version found 1.2.3 (from __init__.py)
      running egg_info
      creating vina.egg-info
      writing vina.egg-info\PKG-INFO
      writing dependency_links to vina.egg-info\dependency_links.txt
      writing requirements to vina.egg-info\requires.txt
      writing top-level names to vina.egg-info\top_level.txt
      writing manifest file 'vina.egg-info\SOURCES.txt'
      Boost library is not installed in this conda environment.
      Traceback (most recent call last):
        File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 363, in <module>
          main()
        File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 177, in get_requires_for_build_wheel
          return self._get_build_requires(
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 159, in _get_build_requires
          self.run_setup()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 174, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 346, in <module>
          setup(
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 148, in setup
          return run_commands(dist)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 163, in run_commands
          dist.run_commands()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 967, in run_commands
          self.run_command(cmd)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\dist.py", line 1214, in run_command
          super().run_command(command)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 986, in run_command
          cmd_obj.run()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 308, in run
          self.find_sources()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 315, in find_sources
          mm.run()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 550, in run
          self.add_defaults()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 587, in add_defaults
          sdist.add_defaults(self)
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 228, in add_defaults
          self._add_defaults_ext()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 311, in _add_defaults_ext
          build_ext = self.get_finalized_command('build_ext')
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 299, in get_finalized_command
          cmd_obj.ensure_finalized()
        File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 107, in ensure_finalized
          self.finalize_options()
        File "setup.py", line 247, in finalize_options
          raise ValueError(error_msg)
      ValueError: Boost library location was not found!
      Directories searched: conda env, /usr/local/include and /usr/include.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
python c++ boost conda
1个回答
1
投票

我也遇到这个错误。我询问 ResearchGate 如何解决这个问题,Cheng Shen 建议 使用 WSL/WSL2 模拟 Linux 环境,然后运行

conda install -c bioconda vina
(或其他类似的命令)

我做了什么。

  1. 在 Windows 上安装 WSL 和 Ubuntu。在 WSL 终端中运行

    code .
    (用于安装 VS Code [推荐])

  2. 按照本指南安装 Anaconda/Miniconda

  3. 在 Ubuntu 终端中输入

    conda install -c bioconda vina

    (bioconda 通道将下载所有必需的软件包 - boost、swig 等)

  4. Vina 应该已成功安装(

    vina --version

     在 WSL 终端中检查)

我发现通过 WSL 安装用于对接的软件包并使用 VS Code 在那里运行脚本要容易得多。这比尝试通过为 Windows 配置 boost 来解决此问题要容易得多。如果您有任何疑问可以在

ResearchGate问我。

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