'Error when installing packages with conda
I am trying to install some pipelines using conda but I'm getting the following error message:
Collecting package metadata (current_repodata.json): failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 438, in _error_catcher
yield
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 764, in read_chunked
self._update_chunk_length()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 694, in _update_chunk_length
line = self._fp.fp.readline()
File "/home/tamer/anaconda3/lib/python3.9/socket.py", line 704, in readinto
return self._sock.recv_into(b)
File "/home/tamer/anaconda3/lib/python3.9/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/home/tamer/anaconda3/lib/python3.9/ssl.py", line 1099, in read
return self._sslobj.read(len, buffer)
ConnectionResetError: [Errno 104] Connection reset by peer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 760, in generate
for chunk in self.raw.stream(chunk_size, decode_content=True):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 572, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 793, in read_chunked
self._original_response.close()
File "/home/tamer/anaconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 455, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
return func(*args, **kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/main_create.py", line 41, in execute
install(args, parser, 'create')
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/install.py", line 259, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 157, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 425, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1020, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/index.py", line 288, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 140, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 132, in <lambda>
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 145, in query
self.load()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 210, in load
_internal_state = self._load()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 375, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 701, in fetch_repodata_remote_request
resp = session.get(join_url(url, filename), headers=headers, proxies=session.proxies,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 542, in get
return self.request('GET', url, **kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 529, in request
resp = self.send(prep, **send_kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 687, in send
r.content
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 838, in content
self._content = b''.join(self.iter_content(CONTENT_CHUNK_SIZE)) or b''
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 763, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))
`$ /home/tamer/anaconda3/bin/conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes`
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/tamer/anaconda3/bin/conda
CONDA_PREFIX=/home/tamer/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/tamer/anaconda3/bin/python
CONDA_ROOT=/home/tamer/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
INFOPATH=/home/linuxbrew/.linuxbrew/share/info:
MANPATH=/home/linuxbrew/.linuxbrew/share/man:
PATH=/home/tamer/anaconda3/bin:/home/tamer/anaconda3/bin:/home/linuxbrew/.l
inuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/tamer/.local/bin:/h
ome/tamer/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:
/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /home/tamer/anaconda3
shell level : 1
user config file : /home/tamer/.condarc
populated config files : /home/tamer/.condarc
conda version : 4.11.0
conda-build version : 3.21.7
python version : 3.9.10.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/tamer/anaconda3 (writable)
conda av data dir : /home/tamer/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/mpi-ie/linux-64
https://conda.anaconda.org/mpi-ie/noarch
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
package cache : /home/tamer/anaconda3/pkgs
/home/tamer/.conda/pkgs
envs directories : /home/tamer/anaconda3/envs
/home/tamer/.conda/envs
platform : linux-64
user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.10 Linux/5.4.0-96-generic ubuntu/20.04.3 glibc/2.31
UID:GID : 1001:1001
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Even when I am updating conda:
$ conda update --all --yes
Collecting package metadata (current_repodata.json): failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 438, in _error_catcher
yield
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 764, in read_chunked
self._update_chunk_length()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 694, in _update_chunk_length
line = self._fp.fp.readline()
File "/home/tamer/anaconda3/lib/python3.9/socket.py", line 704, in readinto
return self._sock.recv_into(b)
File "/home/tamer/anaconda3/lib/python3.9/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/home/tamer/anaconda3/lib/python3.9/ssl.py", line 1099, in read
return self._sslobj.read(len, buffer)
ConnectionResetError: [Errno 104] Connection reset by peer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 760, in generate
for chunk in self.raw.stream(chunk_size, decode_content=True):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 572, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 793, in read_chunked
self._original_response.close()
File "/home/tamer/anaconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/urllib3/response.py", line 455, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
return func(*args, **kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/main_update.py", line 20, in execute
install(args, parser, 'update')
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/cli/install.py", line 259, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 157, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 425, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1020, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/index.py", line 288, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 140, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/home/tamer/anaconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 132, in <lambda>
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 145, in query
self.load()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 210, in load
_internal_state = self._load()
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 375, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "/home/tamer/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 701, in fetch_repodata_remote_request
resp = session.get(join_url(url, filename), headers=headers, proxies=session.proxies,
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 542, in get
return self.request('GET', url, **kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 529, in request
resp = self.send(prep, **send_kwargs)
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/sessions.py", line 687, in send
r.content
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 838, in content
self._content = b''.join(self.iter_content(CONTENT_CHUNK_SIZE)) or b''
File "/home/tamer/anaconda3/lib/python3.9/site-packages/requests/models.py", line 763, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))
`$ /home/tamer/anaconda3/bin/conda update --all --yes`
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/tamer/anaconda3/bin/conda
CONDA_PREFIX=/home/tamer/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/tamer/anaconda3/bin/python
CONDA_ROOT=/home/tamer/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
INFOPATH=/home/linuxbrew/.linuxbrew/share/info:
MANPATH=/home/linuxbrew/.linuxbrew/share/man:
PATH=/home/tamer/anaconda3/bin:/home/tamer/anaconda3/bin:/home/linuxbrew/.l
inuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/tamer/.local/bin:/h
ome/tamer/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:
/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /home/tamer/anaconda3
shell level : 1
user config file : /home/tamer/.condarc
populated config files : /home/tamer/.condarc
conda version : 4.11.0
conda-build version : 3.21.7
python version : 3.9.10.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/tamer/anaconda3 (writable)
conda av data dir : /home/tamer/anaconda3/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 : /home/tamer/anaconda3/pkgs
/home/tamer/.conda/pkgs
envs directories : /home/tamer/anaconda3/envs
/home/tamer/.conda/envs
platform : linux-64
user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.10 Linux/5.4.0-96-generic ubuntu/20.04.3 glibc/2.31
UID:GID : 1001:1001
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
I am trying to use conda to install snakePipes. I tried all the possible solutions on StackOverflow and other platforms but non is working. I am using Ubuntu Ubuntu 20.04.3 LTS (GNU/Linux 5.4.0-96-generic x86_64.
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
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