How to fix the environment with inconsistent dependencies after using conda "update" commands?

Question

I'm trying to update my Spyder to fix some error in my Spyder 3.2.3.

But when I called conda update spyder mentioned in (https://github.com/spyder-ide/spyder/issues/9019#event-2225858161), the Anaconda prompt showed as follow:

and the Spyder wasn't updated to the latest version (3.3.3). I guessed the reason I couldn't update Spyder is because my Conda isn't the latest version, so I ran

conda update -n base -c defaults conda

However after that (update conda to latest version 4.6.11) I found that all my Spyder and my Anaconda Navigator could not be opened. It seems that the commands not only update the Conda, but also update some other packages to py3.7.

When I called conda update spyder again, the prompt showed as follow:

WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - defaults/win-64::anaconda==5.3.1=py37_0
  - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/win-64::anaconda-navigator==1.6.4=py36_0
  - defaults/win-64::astropy==3.0.4=py37hfa6e2cd_0
  - defaults/win-64::blaze==0.11.3=py37_0
  - defaults/win-64::bottleneck==1.2.1=py37h452e1ab_1
  - defaults/win-64::dask==0.19.1=py37_0
  - defaults/win-64::datashape==0.5.4=py37_1
  - defaults/win-64::h5py==2.8.0=py37h3bdd7fb_2
  - defaults/win-64::imageio==2.4.1=py37_0
  - defaults/win-64::matplotlib==2.2.3=py37hd159220_0
  - defaults/win-64::mkl-service==1.1.2=py37hb217b18_5
  - defaults/win-64::mkl_fft==1.0.4=py37h1e22a9b_1
  - defaults/win-64::mkl_random==1.0.1=py37h77b88f5_1
  - defaults/win-64::numba==0.39.0=py37h830ac7b_0
  - defaults/win-64::numexpr==2.6.8=py37h9ef55f4_0
  - defaults/win-64::numpy-base==1.15.1=py37h8128ebf_0
  - defaults/win-64::odo==0.5.1=py37_0
  - defaults/win-64::pandas==0.23.4=py37h830ac7b_0
  - defaults/win-64::patsy==0.5.0=py37_0
  - defaults/win-64::pytables==3.4.4=py37he6f6034_0
  - defaults/win-64::pytest-arraydiff==0.2=py37h39e3cac_0
  - defaults/win-64::pytest-astropy==0.4.0=py37_0
  - defaults/win-64::pytest-doctestplus==0.1.3=py37_0
  - defaults/win-64::pywavelets==1.0.0=py37h452e1ab_0
  - defaults/win-64::scikit-image==0.14.0=py37h6538335_1
  - defaults/win-64::scikit-learn==0.19.2=py37heebcf9a_0
  - defaults/win-64::scipy==1.1.0=py37h4f6bf74_1
  - defaults/win-64::seaborn==0.9.0=py37_0
  - defaults/win-64::statsmodels==0.9.0=py37h452e1ab_0
done
# All requested packages already installed.

I guess maybe the python version conflict (my python version is 3.6.2) causes the exception of the Spyder and Navigator. So I try to restore these packages to py3.6 version by called conda install python = 3.6, but it doesn't works.

This is the result of conda list -version(the last 2 rev)

2019-04-09 22:59:08  (rev 3)
      certifi  {2016.2.28 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 2019.3.9}
      conda  {4.5.13 -> 4.6.11}
      cryptography  {1.8.1 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 2.6.1}
      curl  {7.52.1 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 7.64.0}
      libcurl  {7.61.0 -> 7.64.0}
      libpng  {1.6.34 -> 1.6.36}
      libprotobuf  {3.2.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 3.6.1}
      libssh2  {1.8.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 1.8.0}
      menuinst  {1.4.7 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 1.4.16}
      openssl  {1.0.2l (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 1.1.1b}
      protobuf  {3.2.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 3.6.1}
      pycurl  {7.43.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 7.43.0.2}
      pyqt  {5.6.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 5.9.2}
      python  {3.6.2 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 3.6.8}
      qt  {5.6.2 -> 5.9.7}
      requests  {2.14.2 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 2.21.0}
      sip  {4.18 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 4.19.8}
      sqlite  {3.24.0 -> 3.27.2}
      vc  {14 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free) -> 14.1}
     +krb5-1.16.1

 2019-04-09 23:02:48  (rev 4)
      cryptography  {2.6.1 -> 1.8.1 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      curl  {7.64.0 -> 7.52.1 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      krb5  {1.16.1 -> 1.13.2 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      libcurl  {7.64.0 -> 7.61.1}
      libpng  {1.6.36 -> 1.6.34}
      libprotobuf  {3.6.1 -> 3.2.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      libssh2  {1.8.0 -> 1.8.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      menuinst  {1.4.16 -> 1.4.14}
      openssl  {1.1.1b -> 1.0.2l (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      protobuf  {3.6.1 -> 3.2.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      pycurl  {7.43.0.2 -> 7.43.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      pyqt  {5.9.2 -> 5.6.0 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      python  {3.6.8 -> 3.6.2 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}
      qt  {5.9.7 -> 5.6.2}
      sqlite  {3.27.2 -> 3.25.2}
      vc  {14.1 -> 14 (https://mirrors.ustc.edu.cn/anaconda/pkgs/free)}

This is the result of conda info

     active environment : base
    active env location : C:\Users\lenovo\Anaconda3
            shell level : 1
       user config file : C:\Users\lenovo\.condarc
 populated config files : C:\Users\lenovo\.condarc
          conda version : 4.6.11
    conda-build version : 3.0.19
         python version : 3.6.2.final.0
       base environment : C:\Users\lenovo\Anaconda3  (writable)
           channel URLs : https://mirrors.ustc.edu.cn/anaconda/pkgs/free/win-64
                          https://mirrors.ustc.edu.cn/anaconda/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/win-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\lenovo\Anaconda3\pkgs
                          C:\Users\lenovo\.conda\pkgs
                          C:\Users\lenovo\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\lenovo\Anaconda3\envs
                          C:\Users\lenovo\.conda\envs
                          C:\Users\lenovo\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.6.11 requests/2.21.0 CPython/3.6.2 Windows/10 Windows/10.0.17134
          administrator : False
             netrc file : None
           offline mode : False

What is the best way to fix the issue?

How can I get my Spyder to work again?

Answer 1

This worked with python3.8 and spyder4.1.5:

conda install pyqt --force-reinstall

Answer 2

Fortunately I have fixed my Spyder by using command 'conda install --revision 2', and updated my Spyder to version 3.3.4 in the Anaconda Navigator.

The conda list --version can show each rev before, so I used command conda install --revision 2 to restore the environment to what it was before I updated conda. After that my Spyder and Anaconda Navigator can be used normally. Then I update my Spyder in the Anaconda Navigator to the version 3.3.4.

This is the link of the conda install