Error creating a new environment in Bioconda
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4.1 years ago
Optimist ▴ 190

Please find the error report below and suggest a solution.

Thank You

(base) bio2@dmacsBioLinux8:~$ conda create --name circos_env Collecting package metadata (current_repodata.json): done Solving environment: done

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

Traceback (most recent call last):
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/cli/main_create.py", line 41, in execute
    install(args, parser, 'create')
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 123, in solve_for_transaction
    self._notify_conda_outdated(link_precs)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 970, in _notify_conda_outdated
    SubdirData.query_all(conda_newer_spec, self.channels, self.subdirs,
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 120, in query_all
    result = tuple(concat(executor.map(subdir_query, channel_urls)))
  File "/home/bio2/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
    yield fs.pop().result()
  File "/home/bio2/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
    return self.__get_result()
  File "/home/bio2/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
  File "/home/bio2/miniconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 112, in <lambda>
    subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 125, in query
    self.load()
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 189, in load
    _internal_state = self._load()
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 291, in _load
    _internal_state = self._process_raw_repodata_str(raw_repodata_str)
  File "/home/bio2/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 364, in _process_raw_repodata_str
    json_obj = json.loads(raw_repodata_str or '{}')
  File "/home/bio2/miniconda3/lib/python3.8/json/__init__.py", line 357, in loads
    return _default_decoder.decode(s)
  File "/home/bio2/miniconda3/lib/python3.8/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/bio2/miniconda3/lib/python3.8/json/decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 1 column 91 (char 90)

$ /home/bio2/miniconda3/bin/conda create --name circos_env

environment variables: CIO_TEST=<not set=""> CONDA_DEFAULT_ENV=base CONDA_EXE=/home/bio2/miniconda3/bin/conda CONDA_PREFIX=/home/bio2/miniconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/home/bio2/miniconda3/bin/python CONDA_ROOT=/home/bio2/miniconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE=<not set=""> LD_LIBRARY_PATH= PATH=/home/bio2/miniconda3/bin:/home/bio2/miniconda3/bin:/home/bio2/minicon da3/condabin:/home/bio2/bin:/home/bio2/.local/bin:/home/bio2/bin:/home /bio2/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sb in:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/cd- hit:/usr/lib/cd-hit REQUESTS_CA_BUNDLE=<not set=""> SSL_CERT_FILE=<not set="">

 active environment : base
active env location : /home/bio2/miniconda3
        shell level : 1
   user config file : /home/bio2/.condarc

populated config files : /home/bio2/.condarc conda version : 4.9.0 conda-build version : not installed python version : 3.8.3.final.0 virtual packages : __glibc=2.23=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/bio2/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/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 https://conda.anaconda.org/r/linux-64 https://conda.anaconda.org/r/noarch package cache : /home/bio2/miniconda3/pkgs /home/bio2/.conda/pkgs envs directories : /home/bio2/miniconda3/envs /home/bio2/.conda/envs platform : linux-64 user-agent : conda/4.9.0 requests/2.24.0 CPython/3.8.3 Linux/4.4.0-174-generic ubuntu/16.04.7 glibc/2.23 UID:GID : 1002:1002 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

Bioconda • 1.2k views
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