Collecting package metadata (repodata.json): failed

hongyong_lv · February 3, 2020, 2:19pm

Dear sir,
I came across problem when installing QIIME2 2019.10 on my MacBook.

"
(base) lvxindembp:~ lvxin$ conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-osx-conda.yml
Collecting package metadata (repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/osx-64/repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
‘https://conda.anaconda.org/conda-forge/osx-64’
"

This is an automatically generated error report

"

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

Traceback (most recent call last):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/contrib/pyopenssl.py", line 313, in recv_into
    return self.connection.recv_into(*args, **kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/OpenSSL/SSL.py", line 1840, in recv_into
    self._raise_ssl_error(self._ssl, result)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/OpenSSL/SSL.py", line 1646, in _raise_ssl_error
    raise WantReadError()
OpenSSL.SSL.WantReadError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/contrib/pyopenssl.py", line 313, in recv_into
    return self.connection.recv_into(*args, **kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/OpenSSL/SSL.py", line 1840, in recv_into
    self._raise_ssl_error(self._ssl, result)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/OpenSSL/SSL.py", line 1663, in _raise_ssl_error
    raise SysCallError(errno, errorcode.get(errno))
OpenSSL.SSL.SysCallError: (54, 'ECONNRESET')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 425, in _error_catcher
    yield
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 752, in read_chunked
    self._update_chunk_length()
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 682, in _update_chunk_length
    line = self._fp.fp.readline()
  File "/Users/lvxin/miniconda3/lib/python3.7/socket.py", line 589, in readinto
    return self._sock.recv_into(b)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/contrib/pyopenssl.py", line 328, in recv_into
    return self.recv_into(*args, **kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/contrib/pyopenssl.py", line 318, in recv_into
    raise SocketError(str(e))
OSError: (54, 'ECONNRESET')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/models.py", line 750, in generate
    for chunk in self.raw.stream(chunk_size, decode_content=True):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 560, in stream
    for line in self.read_chunked(amt, decode_content=decode_content):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 781, in read_chunked
    self._original_response.close()
  File "/Users/lvxin/miniconda3/lib/python3.7/contextlib.py", line 130, in __exit__
    self.gen.throw(type, value, traceback)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/urllib3/response.py", line 443, in _error_catcher
    raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ('Connection broken: OSError("(54, \'ECONNRESET\')")', OSError("(54, 'ECONNRESET')"))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1078, in __call__
    return func(*args, **kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 105, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
    prune=getattr(args, 'prune', False), update_modifier=UpdateModifier.FREEZE_INSTALLED)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 262, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 415, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 1004, in _prepare
    self.subdirs, prepared_specs, self._repodata_fn)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/index.py", line 228, in get_reduced_index
    repodata_fn=repodata_fn)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 105, in query_all
    result = tuple(concat(executor.map(subdir_query, channel_urls)))
  File "/Users/lvxin/miniconda3/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
    yield fs.pop().result()
  File "/Users/lvxin/miniconda3/lib/python3.7/concurrent/futures/_base.py", line 435, in result
    return self.__get_result()
  File "/Users/lvxin/miniconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/Users/lvxin/miniconda3/lib/python3.7/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 98, in <lambda>
    package_ref_or_match_spec))
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 110, in query
    self.load()
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 174, in load
    _internal_state = self._load()
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 248, in _load
    repodata_fn=self.repodata_fn)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 485, in fetch_repodata_remote_request
    timeout=timeout)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/sessions.py", line 546, in get
    return self.request('GET', url, **kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/sessions.py", line 533, in request
    resp = self.send(prep, **send_kwargs)
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/sessions.py", line 686, in send
    r.content
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/models.py", line 828, in content
    self._content = b''.join(self.iter_content(CONTENT_CHUNK_SIZE)) or b''
  File "/Users/lvxin/miniconda3/lib/python3.7/site-packages/requests/models.py", line 753, in generate
    raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ('Connection broken: OSError("(54, \'ECONNRESET\')")', OSError("(54, 'ECONNRESET')"))

$ /Users/lvxin/miniconda3/bin/conda-env create -n qiime2-2019.10 --file qiime2-2019.10-py36-osx-conda.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/lvxin/miniconda3/bin/conda
CONDA_PREFIX=/Users/lvxin/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/Users/lvxin/miniconda3/bin/python
CONDA_ROOT=/Users/lvxin/miniconda3
CONDA_SHLVL=1
PATH=/Users/lvxin/miniconda3/bin:/Users/lvxin/miniconda3/bin:/Users/lvxin/m
iniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

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

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"

Nicholas_Bokulich · February 4, 2020, 3:26pm

Hi @hongyong_lv,
Looks like a connection issue:

Maybe just try again? This could be a transient connection issue on your end...