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The following packages will be SUPERSEDED by a higher-priority channel: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!
I had a similar problem, however I solved it. Here is my solution. OS: mac osx
run the following command.
conda install python.app -c conda-forge -v
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...
We just care about the prefix . prefix=/Users/***/opt/anaconda3
you will find lib directory in $prefix/python.app/Contents/
rename lib to lib.bak
install python.app again, you will succeed.
conda install python.app -c conda-forge -v
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