conda安装dnbc4tools环境报错

ZiggeyQi commented 5 months ago

技术老师你好，我用conda env create -f dnbc4tools.yaml -n dnbc4tools配置环境时报错如下： Collecting package metadata (repodata.json): done Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 23.7.4 latest version: 23.11.0

Please update conda by running

$ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

 conda install conda=23.11.0

Downloading and Extracting Packages

Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'. Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0 location of failed script: /gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <==

==> script output <== stdout: stderr: ++ dirname -- /gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/installBiocDataPackage.sh + SCRIPT_DIR=/gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/../share/bioconductor-data-packages + json=/gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/../share/bioconductor-data-packages/dataURLs.json ++ yq '."genomeinfodbdata-1.2.9".fn' /gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/../share/bioconductor-data-packages/dataURLs.json Traceback (most recent call last): File "/gpfs/home/qihansong/anaconda3/envs/dnbc4tools/bin/yq", line 10, in sys.exit(cli()) File "/gpfs/home/qihansong/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/yq/__init__.py", line 63, in cli parser = get_parser(program_name, __doc__) File "/gpfs/home/qihansong/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/yq/parser.py", line 56, in get_parser parser = Parser(**parser_args) TypeError: __init__() got an unexpected keyword argument 'allow_abbrev' + FN= return code: 1 () 更换其他dnbc4tools版本安装也是同样的报错，请问一下这个问题应该如何解决？谢谢。

lishuangshuang0616 commented 5 months ago

尝试将dnbc4tools.yaml前面几行改成这个channel试试

name: dnbc4tools
channels:
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/r/
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
  - http://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
  - http://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
  - bioconda
  - conda-forge
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/
dependencies:

ZiggeyQi commented 5 months ago

尝试了还是不行，可能是服务器网络的原因，换了服务器能正常安装，谢谢你的回复。

MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

conda安装dnbc4tools环境报错 #53