Genovi installation problem

[gaworj]

Hello,

Thank you for a really great tool.

I was able to install it on my laptop at home with Ubuntu 20.04 LTS but failed on Ubuntu workstations.

In the lab I'm using Ubuntu 20.04 LTS: mamba 1.4.9 conda 23.5.2

and 16.04 LTS: mamba 0.25.0 conda 4.14.0

When I tried to install with

pip install genovi

Building wheels for collected packages: genovi Building wheel for genovi (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [87 lines of output] scripts init.py #from .GenoVi import change_background, visualiseGenome, get_args, main #from .addText import addText #from .colors import parseColors #from .create_raw import getArgs, listdir_r, ends_sorted, create_kar, create_feature, base_complete, base, get_categories, create_kar_complete, create_feature_complete, new_loc, write_cog_files, write_lines, createRaw #from .createConf import create_conf, create_conf_main #from .GC_analysis import get_args_, write_content, generate_result, makeGC, createGC #from .genbank2faa import modify_locus, genbankToFaa, mainFaa #from .genbank2fna import gbkToFna, mainFna #from .mergeImages import mergeImages

  #__all__ = ['change_background', 'visualiseGenome', 'get_args', 'main', 'addText', 'parseColors', 'getArgs',
  #                   'listdir_r', 'ends_sorted', 'create_kar', 'create_feature', 'base_complete', 'base', 'get_categories',
  #                   'create_kar_complete', 'create_feature_complete', 'new_loc', 'write_cog_files', 'write_lines',
  #                   'createRaw', 'create_conf', 'create_conf_main', 'get_args_', 'write_content', 'generate_result',
  #                   'makeGC', 'createGC', 'modify_locus', 'genbankToFaa', 'mainFaa', 'gbkToFna', 'mainFna', 'mergeImages',
  #                   '__version__'
  #                   ]
  
  __version__ = '0.4.3'
  
  __all__ = ['__version__']
  
  /home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options
  !!
  
          ********************************************************************************
          Usage of dash-separated 'description-file' will not be supported in future
          versions. Please use the underscore name 'description_file' instead.
  
          By 2024-Sep-26, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.
  
          See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
          ********************************************************************************
  
  !!
    opt = self.warn_dash_deprecation(opt, section)
  Traceback (most recent call last):
    File "<string>", line 36, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-install-76ctju7b/genovi_646f1292e06447638bfedfd88afa8d25/setup.py", line 88, in <module>
      'dev': extra_dev,
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/__init__.py", line 103, in setup
      return distutils.core.setup(**attrs)
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/_distutils/core.py", line 172, in setup
      ok = dist.parse_command_line()
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 475, in parse_command_line
      args = self._parse_command_opts(parser, args)
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/dist.py", line 863, in _parse_command_opts
      nargs = _Distribution._parse_command_opts(self, parser, args)
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 534, in _parse_command_opts
      cmd_class = self.get_command_class(command)
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/dist.py", line 710, in get_command_class
      self.cmdclass[command] = cmdclass = ep.load()
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 208, in load
      module = import_module(match.group('module'))
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/importlib/__init__.py", line 127, in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
    File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
    File "<frozen importlib._bootstrap>", line 983, in _find_and_load
    File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
    File "<frozen importlib._bootstrap_external>", line 728, in exec_module
    File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 28, in <module>
      from .metadata import pkginfo_to_metadata
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/metadata.py", line 16, in <module>
      from .vendored.packaging.requirements import Requirement
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/requirements.py", line 7, in <module>
      from ._parser import parse_requirement as _parse_requirement
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/_parser.py", line 10, in <module>
      from ._tokenizer import DEFAULT_RULES, Tokenizer
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/_tokenizer.py", line 6, in <module>
      from .specifiers import Specifier
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/specifiers.py", line 16, in <module>
      from .utils import canonicalize_version
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/utils.py", line 8, in <module>
      from .tags import Tag, parse_tag
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/tags.py", line 26, in <module>
      from . import _manylinux, _musllinux
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/site-packages/wheel/vendored/packaging/_manylinux.py", line 171, in <module>
      def _get_glibc_version() -> Tuple[int, int]:
    File "/home/jang/miniconda3/envs/genovi/lib/python3.7/functools.py", line 490, in lru_cache
      raise TypeError('Expected maxsize to be an integer or None')
  TypeError: Expected maxsize to be an integer or None
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for genovi Running setup.py clean for genovi Failed to build genovi ERROR: Could not build wheels for genovi, which is required to install pyproject.toml-based projects

Any hints?

Bests, Jan

[cs-di05]

I am having the same issue edit: I managed to install it with the latest python version. However, this raises another error #19

[vsaona]

Hi @gaworj , this pip install genovi was after creating and activating a conda enviroment with circos and Python 3.7?

[gaworj]

Hi, previously I have strictly followed the instructions and started from creating conda env before installing with pip.

Today I repeated the installation procedure in the fresh conda env and everything works fine...

Bests, Jan