similar issue to Yiying with install

[Tim Benke]

I am in ubuntu with gcc and python 3.10 (and other dependencies installed).

It doesnt seem to matter whether or not it's python3.8 or 3.10

Any suggestions appreciated

Thanks

Tim

Processing /tmp/pip-req-build-1h7acw_o/majiq
  Installing build dependencies ... error
  error: subprocess-exited-with-error
 
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [67 lines of output]
      Collecting setuptools>=45
        Using cached setuptools-65.3.0-py3-none-any.whl (1.2 MB)
      Collecting wheel
        Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
      Collecting Cython==0.29.14
        Using cached Cython-0.29.14.tar.gz (2.1 MB)
        Preparing metadata (setup.py): started
        Preparing metadata (setup.py): finished with status 'error'
        error: subprocess-exited-with-error
     
        × python setup.py egg_info did not run successfully.
        │ exit code: 1
        ╰─> [44 lines of output]
            Unable to find pgen, not compiling formal grammar.
            running egg_info
            creating /tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info
            writing /tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info/PKG-INFO
            writing dependency_links to /tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info/dependency_links.txt
            writing entry points to /tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info/entry_points.txt
            writing top-level names to /tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info/top_level.txt
            writing manifest file '/tmp/pip-pip-egg-info-kkrpqx7_/Cython.egg-info/SOURCES.txt'
            Traceback (most recent call last):
              File "<string>", line 2, in <module>
              File "<pip-setuptools-caller>", line 34, in <module>
              File "/tmp/pip-install-6zv36mee/cython_2b4f3ec8d279419aadf772459a15c1d2/setup.py", line 228, in <module>
                setup(
              File "/home/benke/env/lib/python3.10/site-packages/setuptools/__init__.py", line 153, in setup
                return distutils.core.setup(**attrs)
              File "/usr/lib/python3.10/distutils/core.py", line 148, in setup
                dist.run_commands()
              File "/usr/lib/python3.10/distutils/dist.py", line 966, in run_commands
                self.run_command(cmd)
              File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
                cmd_obj.run()
              File "/home/benke/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 299, in run
                self.find_sources()
              File "/home/benke/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 306, in find_sources
                mm.run()
              File "/home/benke/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 541, in run
                self.add_defaults()
              File "/home/benke/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 578, in add_defaults
                sdist.add_defaults(self)
              File "/usr/lib/python3.10/distutils/command/sdist.py", line 228, in add_defaults
                self._add_defaults_ext()
              File "/usr/lib/python3.10/distutils/command/sdist.py", line 311, in _add_defaults_ext
                build_ext = self.get_finalized_command('build_ext')
              File "/usr/lib/python3.10/distutils/cmd.py", line 299, in get_finalized_command
                cmd_obj.ensure_finalized()
              File "/usr/lib/python3.10/distutils/cmd.py", line 107, in ensure_finalized
                self.finalize_options()
              File "/tmp/pip-install-6zv36mee/cython_2b4f3ec8d279419aadf772459a15c1d2/Cython/Distutils/build_ext.py", line 20, in finalize_options
                self.distribution.ext_modules[:] = cythonize(
              File "/tmp/pip-install-6zv36mee/cython_2b4f3ec8d279419aadf772459a15c1d2/Cython/Build/Dependencies.py", line 959, in cythonize
                module_list, module_metadata = create_extension_list(
              File "/tmp/pip-install-6zv36mee/cython_2b4f3ec8d279419aadf772459a15c1d2/Cython/Build/Dependencies.py", line 752, in create_extension_list
                elif isinstance(patterns, basestring) or not isinstance(patterns, collections.Iterable):
            AttributeError: module 'collections' has no attribute 'Iterable'
            [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.
      [end of output]
 
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies 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.

[San Jewell]

Hi Tim,

I am still fairly sure this specific error you have posted is a python3.10 issue, as it only pops up due to the update of the python internal library "collections". (and some of the stable versions of our dependencies do not use the new style imports required by the breaking update)

However, in the meantime, I've created a hotfix that upgrades a number of dependency libraries in the requirements (numpy, cython, and flask) for usage with python3.10.

Please let me know if you are able to install it:

$ pip install git+https://bitbucket.org/biociphers/majiq_aca...@majiq-RC-2.2-hotfix-collections

-San

[Yiying Hu]

Hi Tim,

I am also using ubuntu now. I was using python3.10 in the past. Majiq works for me now.

Here is my solution:

Use conda to build a virtual environment, in my case I call it 'Majiqenv'

$conda create -n Majiqenv python=3.8

Then active this environment

$conda activate Majiqenv

Then install Majiq under this environment.

I hope it also works for you.

Best wishes,

Yiying