error installing conda environment

Post author
Lindsay Romo

I am trying to create a conda environment in a default python jupityr notebook (I need to install several dependencies for a package in the environment that are not installed in the dafault base). I keep getting an error even though I am following the web instructions exactly. How do I fix this? Ultimately I'm trying to install a bunch of packages in the conda environment from requirements.txt. Thanks!

conda create --clone base --prefix /home/jupyter/RBPamp -y
 
Source:      /opt/conda
Destination: /home/jupyter/RBPamp
The following packages cannot be cloned out of the root environment:
 - conda-forge/linux-64::conda-23.7.3-py310hff52083_0
 - file:///tmp/conda/linux-64::dlenv-tf-2-11-gpu-1.0.20230823-py310hfd508a8_0
Packages: 185
Files: 45966

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/conda/lib/python3.10/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
      File "/opt/conda/lib/python3.10/site-packages/conda/cli/main.py", line 64, in main_subshell
        exit_code = do_call(args, parser)
      File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 167, in do_call
        result = getattr(module, func_name)(args, parser)
      File "/opt/conda/lib/python3.10/site-packages/conda/notices/core.py", line 124, in wrapper
        return func(*args, **kwargs)
      File "/opt/conda/lib/python3.10/site-packages/conda/cli/main_create.py", line 50, in execute
        install(args, parser, "create")
      File "/opt/conda/lib/python3.10/site-packages/conda/cli/install.py", line 255, in install
        clone(
      File "/opt/conda/lib/python3.10/site-packages/conda/cli/install.py", line 88, in clone
        actions, untracked_files = clone_env(
      File "/opt/conda/lib/python3.10/site-packages/conda/misc.py", line 314, in clone_env
        symlink(readlink(src), dst)
    FileExistsError: [Errno 17] File exists: '../playwright-core/cli.js' -> '/home/jupyter/RBPamp/share/jupyter/lab/staging/node_modules/.bin/playwright-core'

`$ /opt/conda/bin/conda create --clone base --prefix /home/jupyter/RBPamp -y`

  environment variables:
                 CIO_TEST=<not set>
               CONDA_ROOT=/opt/conda
           CURL_CA_BUNDLE=<not set>
            GATK_ZIP_PATH=/tmp/gatk-4.3.0.0.zip
          LD_LIBRARY_PATH=/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib
                          /server:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/lib/x86_6
                          4-linux-gnu:/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/n
                          vidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda/lib64:/usr/local/cud
                          a/lib:/usr/local/lib/x86_64-linux-gnu:/usr/local/nvidia/lib:/usr/local
                          /nvidia/lib64:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
               LD_PRELOAD=<not set>
             LIBRARY_PATH=/usr/local/cuda/lib64/stubs
                     PATH=/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sb
                          in:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/jupyter/.local/b
                          in:/home/jupyter/packages/bin
               PYTHONPATH=/etc/jupyter/custom:/usr/lib/spark/python:/home/jupyter/packages
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : None
       user config file : /home/jupyter/.condarc
 populated config files : /opt/conda/.condarc
          conda version : 23.7.3
    conda-build version : not installed
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.31=0
                          __linux=6.1.100=0
                          __unix=0=0
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /home/jupyter/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/jupyter/.conda/envs
               platform : linux-64
             user-agent : conda/23.7.3 requests/2.32.3 CPython/3.10.12 Linux/6.1.100+ ubuntu/20.04.6 glibc/2.31
                UID:GID : 1000:100
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install <package>

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install <package>

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Note: you may need to restart the kernel to use updated packages.

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