conda error
1
0
Entering edit mode
2.4 years ago
17318598206 ▴ 20

Hi everyone,

when I use conda to install packages, it shows error:

Collecting package metadata (current_repodata.json): failed

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

    Traceback (most recent call last):
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 704, in fetch_repodata_remote_request
        resp.raise_for_status()
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/requests/mod                                                                                             els.py", line 960, in raise_for_status
        raise HTTPError(http_error_msg, response=self)
    requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://                                                                                             mirrors.aliyun.com/anaconda/cloud/msys2/noarch/current_repodata.json

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/except                                                                                             ions.py", line 1114, in __call__
        return func(*args, **kwargs)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/ma                                                                                             in.py", line 86, in main_subshell
        exit_code = do_call(args, p)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/co                                                                                             nda_argparse.py", line 90, in do_call
        return getattr(module, func_name)(args, parser)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/ma                                                                                             in_install.py", line 20, in execute
        install(args, parser, 'install')
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/in                                                                                             stall.py", line 259, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             olve.py", line 152, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_mod                                                                                             ifier,
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             olve.py", line 195, in solve_for_diff
        final_precs = self.solve_final_state(update_modifier, deps_modifier, pru                                                                                             ne, ignore_pinned,
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             olve.py", line 300, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/common                                                                                             /io.py", line 86, in decorated
        return f(*args, **kwds)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             olve.py", line 463, in _collect_all_metadata
        index, r = self._prepare(prepared_specs)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             olve.py", line 1058, in _prepare
        reduced_index = get_reduced_index(self.prefix, self.channels,
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/i                                                                                             ndex.py", line 287, in get_reduced_index
        new_records = SubdirData.query_all(spec, channels=channels, subdirs=subd                                                                                             irs,
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 139, in query_all
        result = tuple(concat(executor.map(subdir_query, channel_urls)))
      File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.p                                                                                             y", line 611, in result_iterator
        yield fs.pop().result()
      File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.p                                                                                             y", line 439, in result
        return self.__get_result()
      File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.p                                                                                             y", line 388, in __get_result
        raise self._exception
      File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/thread.                                                                                             py", line 57, in run
        result = self.fn(*self.args, **self.kwargs)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 131, in <lambda>
        subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=re                                                                                             podata_fn).query(
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 144, in query
        self.load()
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 209, in load
        _internal_state = self._load()
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 374, in _load
        raw_repodata_str = fetch_repodata_remote_request(
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/s                                                                                             ubdir_data.py", line 735, in fetch_repodata_remote_request
        raise UnavailableInvalidChannel(
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/except                                                                                             ions.py", line 460, in __init__
        body = response.json()
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/requests/mod                                                                                             els.py", line 899, in json
        return complexjson.loads(
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/_                                                                                             _init__.py", line 525, in loads
        return _default_decoder.decode(s)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/d                                                                                             ecoder.py", line 370, in decode
        obj, end = self.raw_decode(s)
      File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/d                                                                                             ecoder.py", line 400, in raw_decode
        return self.scan_once(s, idx=_w(s, idx).end())
    simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

`$ /home/data/vip55/miniconda3/bin/conda install edta`

  environment variables:
                 CIO_TEST=<not set>
        CMAKE_PREFIX_PATH=/home/data/vip55/miniconda3:/home/data/vip55/miniconda                                                                                             3/x86_64-conda-
                          linux-gnu/sysroot/usr
   CONDA_BACKUP_JAVA_HOME=
CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=
      CONDA_BUILD_SYSROOT=/home/data/vip55/miniconda3/x86_64-conda-linux-gnu/sys                                                                                             root
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/home/data/vip55/miniconda3/bin/conda
             CONDA_PREFIX=/home/data/vip55/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/home/data/vip55/miniconda3/bin/python
               CONDA_ROOT=/home/data/vip55/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
     JAVA_LD_LIBRARY_PATH=/home/data/vip55/miniconda3/jre/lib/amd64/server
                     PATH=/home/data/vip55/miniconda3/bin:/home/data/vip55/1work                                                                                             /dev_cell_KAS/KA
                          S-pipe-master/scripts:/home/data/vip55/.aspera/connect                                                                                             /bin:/home/data/
                          vip55/miniconda3/bin:/home/data/vip55/1work/dev_cell_K                                                                                             AS/KAS-pipe-mast
                          er/scripts:/home/data/vip55/.aspera/connect/bin:/home/                                                                                             data/vip55/minic
                          onda3/bin:/home/data/vip55/miniconda3/bin:/home/data/v                                                                                             ip55/miniconda3/
                          condabin:/opt/singularity/3.9.9/bin:/usr/local/sbin:/u                                                                                             sr/local/bin:/us
                          r/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games                                                                                             :/snap/bin:/usr/
                          local/go/bin:/home/data/vip55/sratoolkit.2.9.6-ubuntu6                                                                                             4/bin:/home/data
                          /vip55/gtfToGenePred:/home/data/vip55/.aspera/connect/                                                                                             bin:/home/data/v
                          ip55/sratoolkit.2.9.6-ubuntu64/bin:/home/data/vip55/gt                                                                                             fToGenePred:/hom
                          e/data/vip55/.aspera/connect/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /home/data/vip55/miniconda3
            shell level : 1
       user config file : /home/data/vip55/.condarc
 populated config files : /home/data/vip55/.condarc
          conda version : 4.13.0
    conda-build version : not installed
         python version : 3.8.5.final.0
       virtual packages : __linux=5.8.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/data/vip55/miniconda3  (writable)
      conda av data dir : /home/data/vip55/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://mirrors.aliyun.com/anaconda/pkgs/r/linux-64
                          https://mirrors.aliyun.com/anaconda/pkgs/r/noarch
                          https://mirrors.aliyun.com/anaconda/pkgs/main/linux-64
                          https://mirrors.aliyun.com/anaconda/pkgs/main/noarch
                          https://mirrors.aliyun.com/anaconda/cloud/bioconda/lin                                                                                             ux-64
                          https://mirrors.aliyun.com/anaconda/cloud/bioconda/noa                                                                                             rch
                          https://mirrors.aliyun.com/anaconda/cloud/msys2/linux-                                                                                             64
                          https://mirrors.aliyun.com/anaconda/cloud/msys2/noarch
          package cache : /home/data/vip55/miniconda3/pkgs
                          /home/data/vip55/.conda/pkgs
       envs directories : /home/data/vip55/miniconda3/envs
                          /home/data/vip55/.conda/envs
               platform : linux-64
             user-agent : conda/4.13.0 requests/2.27.1 CPython/3.8.5 Linux/5.8.0                                                                                             -36-generic ubuntu/20.04.4 glibc/2.31
                UID:GID : 1056:1057
             netrc file : None
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
Upload did not complete.

How can I solve it? Thank you
conda • 1.9k views
ADD COMMENT •
0
Entering edit mode

This is not related to bioinformatics. For the future, you are not helping yourself or us by not telling us the package you want to install, and by not properly formatting the error message.

ADD REPLY •
0
Entering edit mode

When I install all packages by conda, I get the same error

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

Traceback (most recent call last):
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 704, in fetch_repodata_remote_request
    resp.raise_for_status()
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/requests/models.py", line 960, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://mirrors.aliyun.com/anaconda/cloud/msys2/noarch/current_repodata.json

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1114, in __call__
    return func(*args, **kwargs)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 86, in main_subshell
    exit_code = do_call(args, p)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 90, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 259, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 195, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 300, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 86, in decorated
    return f(*args, **kwds)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 463, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 1058, in _prepare
    reduced_index = get_reduced_index(self.prefix, self.channels,
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/index.py", line 287, in get_reduced_index
    new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 139, in query_all
    result = tuple(concat(executor.map(subdir_query, channel_urls)))
  File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
    yield fs.pop().result()
  File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
  File "/home/data/vip55/miniconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 131, in <lambda>
    subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 144, in query
    self.load()
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 209, in load
    _internal_state = self._load()
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 374, in _load
    raw_repodata_str = fetch_repodata_remote_request(
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 735, in fetch_repodata_remote_request
    raise UnavailableInvalidChannel(
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 460, in __init__
    body = response.json()
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/requests/models.py", line 899, in json
    return complexjson.loads(
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/__init__.py", line 525, in loads
    return _default_decoder.decode(s)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/decoder.py", line 370, in decode
    obj, end = self.raw_decode(s)
  File "/home/data/vip55/miniconda3/lib/python3.8/site-packages/simplejson/decoder.py", line 400, in raw_decode
    return self.scan_once(s, idx=_w(s, idx).end())
simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

$ /home/data/vip55/miniconda3/bin/conda install -c bioconda -c conda-forge edta

environment variables: CIO_TEST=<not set> CMAKE_PREFIX_PATH=/home/data/vip55/miniconda3:/home/data/vip55/miniconda3/x86_64-conda- linux-gnu/sysroot/usr CONDA_BACKUP_JAVA_HOME= CONDA_BACKUP_JAVA_LD_LIBRARY_PATH= CONDA_BUILD_SYSROOT=/home/data/vip55/miniconda3/x86_64-conda-linux-gnu/sysroot CONDA_DEFAULT_ENV=base CONDA_EXE=/home/data/vip55/miniconda3/bin/conda CONDA_PREFIX=/home/data/vip55/miniconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/home/data/vip55/miniconda3/bin/python CONDA_ROOT=/home/data/vip55/miniconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE=<not set> JAVA_LD_LIBRARY_PATH=/home/data/vip55/miniconda3/jre/lib/amd64/server PATH=/home/data/vip55/miniconda3/bin:/home/data/vip55/1work/dev_cell_KAS/KA S-pipe-master/scripts:/home/data/vip55/.aspera/connect/bin:/home/data/ vip55/miniconda3/bin:/home/data/vip55/miniconda3/bin:/home/data/vip55/ miniconda3/condabin:/opt/singularity/3.9.9/bin:/usr/local/sbin:/usr/lo cal/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/sna p/bin:/usr/local/go/bin:/home/data/vip55/sratoolkit.2.9.6-ubuntu64/bin :/home/data/vip55/gtfToGenePred:/home/data/vip55/.aspera/connect/bin REQUESTS_CA_BUNDLE=<not set> SSL_CERT_FILE=<not set>

 active environment : base
active env location : /home/data/vip55/miniconda3
        shell level : 1
   user config file : /home/data/vip55/.condarc

populated config files : /home/data/vip55/.condarc conda version : 4.13.0 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : __linux=5.8.0=0 __glibc=2.31=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/data/vip55/miniconda3 (writable) conda av data dir : /home/data/vip55/miniconda3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://mirrors.aliyun.com/anaconda/pkgs/r/linux-64 https://mirrors.aliyun.com/anaconda/pkgs/r/noarch https://mirrors.aliyun.com/anaconda/pkgs/main/linux-64 https://mirrors.aliyun.com/anaconda/pkgs/main/noarch https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64 https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch https://mirrors.aliyun.com/anaconda/cloud/msys2/linux-64 https://mirrors.aliyun.com/anaconda/cloud/msys2/noarch package cache : /home/data/vip55/miniconda3/pkgs /home/data/vip55/.conda/pkgs envs directories : /home/data/vip55/miniconda3/envs /home/data/vip55/.conda/envs platform : linux-64 user-agent : conda/4.13.0 requests/2.27.1 CPython/3.8.5 Linux/5.8.0-36-generic ubuntu/20.04.4 glibc/2.31 UID:GID : 1056:1057 netrc file : None offline mode : False

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

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0
Entering edit mode
2.4 years ago
svp ▴ 680

check your internet connection as it shows 404 Client Error: Not Found for url:

Also try,

pip install edta
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Entering edit mode

it is a conda package, no python module

ADD REPLY •
0
Entering edit mode

if that's the case try: conda install -c bioconda edta

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Entering edit mode

No effect, still an same error

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