New problem

[Yiying Hu]

Hi,

I tried to use linux system to install, and got this errer:

Cloning https://bitbucket.org/biociphers/majiq_academic.git to /tmp/pip-req-build-oav10yqw
  Running command git clone --filter=blob:none --quiet https://bitbucket.org/biociphers/majiq_academic.git /tmp/pip-req-build-oav10yqw
  warning: filtering not recognized by server, ignoring
  Resolved https://bitbucket.org/biociphers/majiq_academic.git to commit 85d07819f55b182c830bdc69296c1485f51b3100
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Processing /tmp/pip-req-build-oav10yqw/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-63.4.1-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-acntjbc9/Cython.egg-info
            writing /tmp/pip-pip-egg-info-acntjbc9/Cython.egg-info/PKG-INFO
            writing dependency_links to /tmp/pip-pip-egg-info-acntjbc9/Cython.egg-info/dependency_links.txt
            writing entry points to /tmp/pip-pip-egg-info-acntjbc9/Cython.egg-info/entry_points.txt
            writing top-level names to /tmp/pip-pip-egg-info-acntjbc9/Cython.egg-info/top_level.txt
            writing manifest file '/tmp/pip-pip-egg-info-acntjbc9/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-bmyqsq6x/cython_46d305bab7604d149ba50d9d2ac4b719/setup.py", line 228, in <module>
                setup(
              File "/home/yiying/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/yiying/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 299, in run
                self.find_sources()
              File "/home/yiying/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 306, in find_sources
                mm.run()
              File "/home/yiying/env/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 541, in run
                self.add_defaults()
              File "/home/yiying/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-bmyqsq6x/cython_46d305bab7604d149ba50d9d2ac4b719/Cython/Distutils/build_ext.py", line 20, in finalize_options
                self.distribution.ext_modules[:] = cythonize(
              File "/tmp/pip-install-bmyqsq6x/cython_46d305bab7604d149ba50d9d2ac4b719/Cython/Build/Dependencies.py", line 959, in cythonize
                module_list, module_metadata = create_extension_list(
              File "/tmp/pip-install-bmyqsq6x/cython_46d305bab7604d149ba50d9d2ac4b719/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.

Thank you very much for your help.

Best wishes,

Yiying

[Paul Jewell]

Hi Yiying,

The issue comes from a deprecation issued in python3.10 for collections.iterable. In this case the stable version of cython (dependency package for majiq) does not have this correction. I see two solutions you can try in the moment:

-Use the majiq supported python version (3.8) instead of 3.10

-Try to change Cython==0.29.14 in requirements.txt to just Cython, which will use a more recent version of cython which should have the deprecation fixed (but is not tested for stability with majiq yet)

Let me know if you are able to try either of these or need additional information.

Thanks!

-San

[San Jewell]

Hi Yiying,

Please also check the new solution I posted on https://groups.google.com/g/majiq_voila/c/NcjMYJiAjy0 if the above suggestions don't immediately work for you.

Thanks,

-San

[Yiying Hu]

Hi San,

Thank you very much for you help. It works now.

Best wishes,

Yiying