错误 conda.core.link:_execute(701)：更新 conda 包时出错

Question

I'm having trouble trying to update my base conda environment. Does anyone know how to resolve this issue?

conda update -n base --all

It returns:

Collecting package metadata (current_repodata.json): done
Solving environment: \ 
Warning: 2 possible package resolutions (only showing differing packages):
  - conda-forge/noarch::sphinx-3.5.3-pyhd8ed1ab_0, conda-forge/osx-64::docutils-0.17-py37hf985489_0
  - conda-forge/noarch::sphinx-3.5.4-pyh44b312d_0, conda-forge/osx-64::docutils-0.15.2-py37hf985489done

## Package Plan ##

  environment location: /Users/winkulvichit/miniconda3


The following NEW packages will be INSTALLED:

  argon2-cffi        conda-forge/osx-64::argon2-cffi-20.1.0-py37hf967b71_2
  lcms2              conda-forge/osx-64::lcms2-2.12-h577c468_0
  libdeflate         conda-forge/osx-64::libdeflate-1.7-h35c211d_5
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  openjpeg           conda-forge/osx-64::openjpeg-2.4.0-h6cbf5cd_0
  pillow             conda-forge/osx-64::pillow-8.1.2-py37hd4e48bc_1
  seaborn-base       conda-forge/noarch::seaborn-base-0.11.1-pyhd8ed1ab_1

The following packages will be UPDATED:

  apscheduler                          3.6.3-py37hc8dfbb8_1 --> 3.7.0-py37hf985489_0
  bzip2                                    1.0.8-h0b31af3_2 --> 1.0.8-hc929b4f_4
  htslib                                              1.3-0 --> 1.12-hc38c3fb_1
  jupyter            conda-forge/noarch::jupyter-1.0.0-py_2 --> conda-forge/osx-64::jupyter-1.0.0-py37hf985489_6
  libllvm9                                 9.0.1-h7475705_1 --> 9.0.1-h223d4b2_3
  matplotlib                                        3.2.1-0 --> 3.4.1-py37hf985489_0
  matplotlib-base                      3.2.1-py37hddda452_0 --> 3.4.1-py37hb018525_0
  notebook           conda-forge/osx-64::notebook-6.0.3-py~ --> conda-forge/noarch::notebook-6.3.0-pyha770c72_1
  r-irkernel                              1.1-r40h6115d3f_1 --> 1.1.1-r40h6115d3f_0
  samtools                                          1.3.1-0 --> 1.12-hfcfc997_1
  scikit-learn                        0.23.1-py37hf5857e7_0 --> 0.24.1-py37hbcf18d0_0
  seaborn                                       0.10.1-py_0 --> 0.11.1-hd8ed1ab_1
  spyder-terminal    spyder-ide::spyder-terminal-0.3.1-py3~ --> conda-forge::spyder-terminal-0.5.0-py37hf985489_2

The following packages will be SUPERSEDED by a higher-priority channel:

  python.app                 pkgs/main::python.app-2-py37_9 --> conda-forge::python.app-1.3-py37hf967b71_4

The following packages will be DOWNGRADED:

  tzlocal                                  2.1-pyh9f0ad1d_0 --> 2.0.0-py_0


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(701): An error occurred while installing package 'conda-forge::python.app-1.3-py37hf967b71_4'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::python.app-1.3-py37hf967b71_4
location of failed script: /Users/winkulvichit/miniconda3/bin/.python.app-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: ln: ./lib: File exists

return code: 1

()

I couldn't find any solutions on the internet. If there is any way to fix this issue without having to reinstall conda would be appreciated. Thank you!

Answer 1

I had a similar problem, however I solved it. Here is my solution. OS: mac osx

1. run the following command.

   conda install python.app -c conda-forge -v

2. In the output, you will find the following content

   Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... ===> UNLINKING PACKAGE: https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/osx-64::certifi-2021.10.8-py37hecd8cb5_0 <===

   prefix=/Users/huaweiwang/opt/anaconda3 ===> LINKING PACKAGE: conda-forge::certifi-2021.10.8-py37hf985489_0 <===

   prefix=/Users/* /opt/anaconda3 source=/Users/ /opt/anaconda3/pkgs/certifi-2021.10.8-py37hf985489_0...

3. We just care about the prefix . prefix=/Users/***/opt/anaconda3

4. you will find lib directory in $prefix/python.app/Contents/

5. rename lib to lib.bak

6. install python.app again, you will succeed.

   conda install python.app -c conda-forge -v