anaconda – Can’t update conda after 3 years away

admin

I am primarily a molecular biologist and an infrequent bioinformatician. After three years of collecting samples I back to analyzing them using my university’s cluster.

Unfortunately, I logged into my account and after typing conda update conda I got the following error:

$ conda update conda
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ..........An unexpected error has occurred, please consider sending the
following traceback to the conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Include the output of the command 'conda info' in your report.


Traceback (most recent call last):
  File "/home/agarbuzov/anaconda2/bin/conda", line 6, in <module>
    sys.exit(main())
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/cli/main.py", line 120, in main
    exit_code = args_func(args, p)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/cli/main.py", line 130, in args_func
    exit_code = args.func(args, p)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/cli/main_update.py", line 64, in execute
    install(args, parser, 'update')
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/cli/install.py", line 231, in install
    index = common.get_index_trap(**index_args)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/cli/common.py", line 622, in get_index_trap
    return get_index(*args, **kwargs)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/api.py", line 26, in get_index
    index = fetch_index(channel_urls, use_cache=use_cache, unknown=unknown)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/fetch.py", line 293, in fetch_index
    repodatas = [(u, f.result()) for u, f in zip(urls, futures)]
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/concurrent/futures/_base.py", line 398, in result
    return self.__get_result()
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/concurrent/futures/thread.py", line 55, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/fetch.py", line 68, in func
    res = f(*args, **kwargs)
  File "/home/agarbuzov/anaconda2/lib/python2.7/site-packages/conda/fetch.py", line 117, in fetch_repodata
    cache = json.loads(json_str)
  File "/home/agarbuzov/anaconda2/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/agarbuzov/anaconda2/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/agarbuzov/anaconda2/lib/python2.7/json/decoder.py", line 380, in raw_decode
    obj, end = self.scan_once(s, idx)
MemoryError 

$ conda info
Using Anaconda Cloud api site https://api.anaconda.org
Current conda install:

             platform : linux-64
        conda version : 4.1.6
    conda-env version : 2.5.1
  conda-build version : 1.21.3
       python version : 2.7.12.final.0
     requests version : 2.10.0
     root environment : /home/agarbuzov/anaconda2  (writable)
  default environment : /home/agarbuzov/anaconda2
     envs directories : /home/agarbuzov/anaconda2/envs
        package cache : /home/agarbuzov/anaconda2/pkgs
         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://repo.continuum.io/pkgs/free/linux-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/linux-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : /home/agarbuzov/.condarc
         offline mode : False
    is foreign system : False

Can somebody help me out? I have no idea why this is suddenly broken. Thank you in advance!

I’m not sure what to try at this point.

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