zyxue / ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages
MIT License
140 stars 29 forks source link

Error in installation #21

Closed binitl closed 2 years ago

binitl commented 2 years ago

Dear Zyxue, I am trying to install the program but getting the following error message. My python version is 3.10.2.

Keyring is skipped due to an exception: module 'collections' has no attribute 'MutableMapping'
Defaulting to user installation because normal site-packages is not writeable
Collecting ncbitax2lin
  Using cached ncbitax2lin-2.2.0-py3-none-any.whl (10 kB)
Collecting pandas<2.0.0,>=1.0.3
  Using cached pandas-1.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
Collecting typing-extensions<4.0.0,>=3.7.4
  Using cached typing_extensions-3.10.0.2-py3-none-any.whl (26 kB)
Collecting fire<0.4.0,>=0.3.1
  Using cached fire-0.3.1.tar.gz (81 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [20 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 14, in <module>
        File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 12, in <module>
          import setuptools.version
        File "/usr/lib/python3/dist-packages/setuptools/version.py", line 1, in <module>
          import pkg_resources
        File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 77, in <module>
          __import__('pkg_resources.extern.packaging.requirements')
        File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", line 9, in <module>
          from pkg_resources.extern.pyparsing import stringStart, stringEnd, originalTextFor, ParseException
        File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 672, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 632, in _load_backward_compatible
        File "/usr/lib/python3/dist-packages/pkg_resources/extern/__init__.py", line 43, in load_module
          __import__(extant)
        File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", line 943, in <module>
          collections.MutableMapping.register(ParseResults)
      AttributeError: module 'collections' has no attribute 'MutableMapping'
      [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.
zyxue commented 2 years ago

Hey binitl, ncbitax2lin doesn't support python-3.10 yet, but I just updated it to support python-3.9, could you py39 instead? Make sure to get the latest version with pip install -U ncbitax2lin