安装RSeQC时pyBigWig的setup.py运行报错（Win10 Python3.8）

问题背景 #

• 安装场景：在conda创建的Python 3.8虚拟环境中安装RSeQC，操作系统为Windows 10 Pro
• 报错触发阶段：pip安装到依赖pyBigWig，执行setup.py生成元数据阶段失败
• 核心报错信息：

AttributeError: 'NoneType' object has no attribute 'split'

报错位置为pyBigWig安装包的setup.py第24行，代码尝试读取sysconfig.get_config_vars('BLDLIBRARY')的返回值并做分割操作，但该接口在当前环境返回了空值None，导致流程中断。

完整终端执行日志如下：

(python3.8) C:\Users\me>pip --version
pip 22.1.2 from C:\Users\me\Anaconda3\envs\python3.8\lib\site-packages\pip (python 3.8)

(python3.8) C:\Users\me>pip install RSeQC
Collecting RSeQC
  Downloading RSeQC-4.0.0-py3-none-any.whl (133 kB)
     ---------------------------------------- 133.6/133.6 kB 438.8 kB/s eta 0:00:00
Collecting bx-python
  Downloading bx-python-0.8.13.tar.gz (1.4 MB)
     ---------------------------------------- 1.4/1.4 MB 1.0 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting cython>=0.17
  Using cached Cython-0.29.30-py2.py3-none-any.whl (985 kB)
Collecting pyBigWig
  Downloading pyBigWig-0.3.18.tar.gz (64 kB)
     ---------------------------------------- 64.8/64.8 kB 699.9 kB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\me\AppData\Local\Temp\pip-install-j0xpd3pz\pybigwig_d3408484097f434884b2c8954968140e\setup.py", line 24, in <module>
          for e in sysconfig.get_config_vars('BLDLIBRARY')[0].split():
      AttributeError: 'NoneType' object has no attribute 'split'
      [end of output]

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

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

解决方法 #

• 优先使用conda安装pyBigWig预编译包，避开pip源码编译的适配问题：
  1. 激活当前Python 3.8的conda虚拟环境
  2. 执行命令conda install -c bioconda pybigwig，等待安装完成，该渠道提供的包已经提前完成Windows平台编译，不会出现配置变量缺失的问题
  3. pyBigWig安装完成后，再执行pip install RSeQC即可完成全部安装
• 若必须使用pip安装，先补全编译依赖：
  在虚拟环境中执行conda install libpython m2w64-toolchain cython，安装Windows平台下C扩展编译所需的工具链和配置文件，修复sysconfig中BLDLIBRARY变量为空的问题，之后再执行pip安装命令即可。

注意：Windows平台下安装带C扩展的生物信息学类Python包时，尽量优先使用bioconda源的预编译版本，直接用pip从源码编译大概率会遇到各类环境配置、依赖缺失的问题。

内容的提问来源于stack exchange，提问作者Giamma Fer