ubuntu18安装python接口的openslide过程和错误整理

配置

包	版本
python	3.6.10
pip	20.1

安装过程

pip直接安装

pip install openslide-python

出现问题：

ERROR: Command errored out with exit status 1:
     command: /media/s2/cyq/anaconda3/envs/keras/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kpd80yg0/openslide-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kpd80yg0/openslide-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-86l6dxk_
         cwd: /tmp/pip-install-kpd80yg0/openslide-python/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-kpd80yg0/openslide-python/setup.py", line 2, in <module>
        from setuptools import setup, Extension, Feature
    ImportError: cannot import name 'Feature'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

安装openslide依赖：

sudo apt install python-opendslide

还是一样的问题

试了几种办法都不管用（包括升级python版本，重新搭一个虚拟环境等），最后选择用tar.gz安装

openslide下载网址：OpenSlide

选择python接口下载，我选择的最新版本1.1.1
上传到集群，解压：
tar -xzvf openslide-python-1.1.1.tar.gz
进入文件夹：
cd openslide-python-1.1.1/
安装：
python setup.py install --single-version-externally-managed --record /dev/null
出现错误：

Traceback (most recent call last):
  File "setup.py", line 2, in <module>
    from setuptools import setup, Extension, Feature
ImportError: cannot import name 'Feature' from 'setuptools' (/media/s2/cyq/anaconda3/envs/test/lib/python3.8/site-packages/setuptools/__init__.py)

解决办法：降低setuptools版本（原来是46.3.1）
pip install setuptools==45
再次安装：
python setup.py install --single-version-externally-managed --record /dev/null
出现信息：

……
running install_egg_info
running egg_info
writing openslide_python.egg-info/PKG-INFO
writing dependency_links to openslide_python.egg-info/dependency_links.txt
writing requirements to openslide_python.egg-info/requires.txt
writing top-level names to openslide_python.egg-info/top_level.txt
reading manifest file 'openslide_python.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'openslide_python.egg-info/SOURCES.txt'
Copying openslide_python.egg-info to /media/s2/cyq/anaconda3/envs/test/lib/python3.8/site-packages/openslide_python-1.1.1-py3.8.egg-info
running install_scripts
writing list of installed files to '/dev/null'

测试，结果报错：

(test) cyq@node5-SYS-4029GP-TRT:~/openslide-python-1.1.1$ python
Python 3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openslide
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/media/s2/cyq/openslide-python-1.1.1/openslide/__init__.py", line 29, in <module>
    from openslide import lowlevel
  File "/media/s2/cyq/openslide-python-1.1.1/openslide/lowlevel.py", line 58, in <module>
    _lib = cdll.LoadLibrary('libopenslide.so.0')
  File "/media/s2/cyq/anaconda3/envs/test/lib/python3.8/ctypes/__init__.py", line 451, in LoadLibrary
    return self._dlltype(name)
  File "/media/s2/cyq/anaconda3/envs/test/lib/python3.8/ctypes/__init__.py", line 373, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libopenslide.so.0: cannot open shared object file: No such file or directory
>>> 

上网查了说是缺少依赖，需要安装：
sudo apt-get install openslide-tools
报错：

root@node5-SYS-4029GP-TRT:~# sudo apt-get install openslide-tools
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  libopenjp2-7 libopenslide0
Suggested packages:
  libtiff-tools
The following NEW packages will be installed:
  libopenjp2-7 libopenslide0 openslide-tools
0 upgraded