TypeError: '<' not supported between instances of 'PrefixRecord' and 'PackageRecord' while updating Conda

Question

I tried to update conda by using "conda update conda" and "conda update --all". However, I kept getting the below message. Does anyone know what happened here?

Collecting package metadata (repodata.json): done Solving environment: - The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency:

• defaults/osx-64::conda-build==3.10.5=py36_0
• defaults/osx-64::anaconda-navigator==1.9.7=py36_0
• defaults/osx-64::anaconda-client==1.6.14=py36_0
• defaults/osx-64::numpydoc==0.8.0=py36_0
• defaults/osx-64::spyder==3.2.8=py36_0
• defaults/osx-64::blaze==0.11.3=py36h02e7a37_0
• defaults/osx-64::anaconda==5.2.0=py36_3
• defaults/osx-64::anaconda-project==0.8.2=py36h9ee5d53_0
• defaults/osx-64::sphinx==1.7.4=py36_0
• defaults/osx-64::conda==4.7.5=py36_0 done

">>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<"

Traceback (most recent call last):
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 252, in _topo_sort_handle_cycles
    value = next(t)
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 230, in _toposort_raise_on_cycles
    raise CyclicalDependencyError(tuple(graph))
conda.exceptions.CyclicalDependencyError: Cyclic dependencies exist among these items: 
  - defaults::_anaconda_depends-2019.03-py36_0
  - defaults::anaconda-custom-py36_1
  - defaults::astropy-3.2.1-py36h1de35cc_0
  - defaults::bkcharts-0.2-py36h073222e_0
  - defaults::bokeh-1.2.0-py36_0
  - defaults::bottleneck-1.2.1-py36h1d22016_1
  - defaults::dask-2.0.0-py_0
  - defaults::datashape-0.5.4-py36_1
  - defaults::h5py-2.9.0-py36h3134771_0
  - defaults::imageio-2.5.0-py36_0
  - defaults::lightgbm-2.2.1-py36h0a44026_0
  - defaults::matplotlib-3.1.0-py36h54f8f79_0
  - defaults::mkl-service-2.0.2-py36h1de35cc_0
  - defaults::mkl_fft-1.0.12-py36h5e564d8_0
  - defaults::numba-0.44.1-py36h6440ff4_0
  - defaults::numexpr-2.6.9-py36h7413580_0
  - defaults::numpy-1.16.4-py36hacdab7b_0
  - defaults::odo-0.5.1-py36hc1af34a_0
  - defaults::pandas-0.24.2-py36h0a44026_0
  - defaults::patsy-0.5.1-py36_0
  - defaults::pytables-3.5.2-py36h5bccee9_1
  - defaults::pytest-arraydiff-0.3-py36h39e3cac_0
  - defaults::pytest-astropy-0.5.0-py36_0
  - defaults::pytest-doctestplus-0.3.0-py36_0
  - defaults::pywavelets-1.0.3-py36h1d22016_1
  - defaults::scikit-image-0.15.0-py36h0a44026_0
  - defaults::scikit-learn-0.21.2-py36h27c97d8_0
  - defaults::scipy-1.2.1-py36h1410ff5_0
  - defaults::seaborn-0.9.0-py36_0
  - defaults::statsmodels-0.10.0-py36h1d22016_0
  - defaults::blaze-0.11.3-py36h02e7a37_0
  - defaults::scipy-1.1.0-py36hcaad992_0
  - defaults::numexpr-2.6.5-py36h057f876_0
  - defaults::astropy-3.0.2-py36h917ab60_1
  - defaults::bokeh-0.12.16-py36_0
  - defaults::matplotlib-2.2.2-py36ha7267d0_0
  - defaults::patsy-0.5.0-py36_0
  - defaults::pywavelets-0.5.2-py36h2710a04_0
  - defaults::dask-0.17.5-py36_0
  - defaults::pytest-astropy-0.3.0-py36_0
  - defaults::mkl_random-1.0.1-py36h78cc56f_0
  - defaults::pytables-3.4.3-py36h5ca999c_2
  - defaults::numpy-1.14.3-py36h9bb19eb_1
  - defaults::bottleneck-1.2.1-py36hbd380ad_0
  - defaults::pytest-doctestplus-0.1.3-py36_0
  - defaults::pytest-arraydiff-0.2-py36_0
  - defaults::h5py-2.7.1-py36ha8ecd60_2
  - defaults::datashape-0.5.4-py36hfb22df8_0
  - defaults::pandas-0.23.0-py36h1702cab_0
  - defaults::seaborn-0.8.1-py36h595ecd9_0
  - defaults::numba-0.38.0-py36h1702cab_0
  - defaults::mkl_fft-1.0.1-py36h917ab60_0
  - defaults::scikit-image-0.13.1-py36h1de35cc_1
  - defaults::statsmodels-0.9.0-py36h917ab60_0
  - defaults::imageio-2.3.0-py36_0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1043, in __call__
    return func(*args, **kwargs)
  File "/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/anaconda3/lib/python3.6/site-packages/conda/cli/main_update.py", line 20, in execute
    install(args, parser, 'update')
  File "/anaconda3/lib/python3.6/site-packages/conda/cli/install.py", line 280, in install
    force_reinstall=context.force_reinstall or context.force,
  File "/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 112, in solve_for_transaction
    force_remove, force_reinstall)
  File "/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 150, in solve_for_diff
    force_remove)
  File "/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 261, in solve_final_state
    ssc.solution_precs = IndexedSet(PrefixGraph(ssc.solution_precs).graph)
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 47, in __init__
    self._toposort()
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 202, in _toposort
    sorted_nodes = tuple(self._topo_sort_handle_cycles(graph_copy))
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 259, in _topo_sort_handle_cycles
    yield cls._toposort_pop_key(graph)
  File "/anaconda3/lib/python3.6/site-packages/conda/models/prefix_graph.py", line 274, in _toposort_pop_key
    (len(parents), node.name, node) for node, parents in iteritems(graph)
TypeError: '<' not supported between instances of 'PrefixRecord' and 'PackageRecord'

Answer 1

I fixed mine by using conda install -c anaconda setuptools, and then conda update conda.

Answer 2

It is a known issue which was already fixed, you can read about it at github https://github.com/conda/conda/issues/8898 as for the quick fix, run the commands below:

conda remove --name base anaconda
conda update --all