I am trying to install seqvec via bioembeddings using pip install bioembedding[seqvec]. I have installed python 3.7.13 before installing bio embedding. I am encountering this error.
ERROR: Exception:
Traceback (most recent call last):
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
yield
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
File "/home/.conda/envs/bioembed1/lib/python3.7/http/client.py", line 465, in read
n = self.readinto(b)
File "/home/.conda/envs/bioembed1/lib/python3.7/http/client.py", line 509, in readinto
n = self.fp.readinto(b)
File "/home/.conda/envs/bioembed1/lib/python3.7/socket.py", line 589, in readinto
return self._sock.recv_into(b)
File "/home/.conda/envs/bioembed1/lib/python3.7/ssl.py", line 1071, in recv_into
return self.read(nbytes, buffer)
File "/home/.conda/envs/bioembed1/lib/python3.7/ssl.py", line 929, in read
return self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
status = run_func(*args)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
return func(self, options, args)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 378, in run
reqs, check_supported_wheels=not options.target_dir
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve
collected.requirements, max_rounds=limit_how_complex_resolution_can_be
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 427, in resolve
failure_causes = self._attempt_to_pin_criterion(name)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 239, in _attempt_to_pin_criterion
criteria = self._get_updated_criteria(candidate)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 230, in _get_updated_criteria
self._add_to_criteria(criteria, requirement, parent=candidate)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
if not criterion.candidates:
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in bool
return bool(self._sequence)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in bool
return any(self)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in
return (c for c in iterator if id(c) not in self._incompatible_ids)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
candidate = func()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 183, in _make_candidate_from_link
link, template, name, version
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link
version=version,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 296, in init
version=version,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in init
self.dist = self._prepare()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare
dist = self._prepare_distribution()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 519, in prepare_linked_requirement
metadata_dist = self._fetch_metadata_only(req)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 372, in _fetch_metadata_only
req
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 394, in _fetch_metadata_using_link_data_attr
hashes=metadata_link.as_hashes(),
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 109, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/network/download.py", line 147, in call
for chunk in chunks:
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/network/utils.py", line 87, in response_chunks
decode_content=False,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 587, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/home/.conda/envs/bioembed1/lib/python3.7/contextlib.py", line 130, in exit
self.gen.throw(type, value, traceback)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.
I am trying to install seqvec via bioembeddings using pip install bioembedding[seqvec]. I have installed python 3.7.13 before installing bio embedding. I am encountering this error.
ERROR: Exception: Traceback (most recent call last): File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher yield File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 561, in read data = self._fp_read(amt) if not fp_closed else b"" File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 98, in read data: bytes = self.__fp.read(amt) File "/home/.conda/envs/bioembed1/lib/python3.7/http/client.py", line 465, in read n = self.readinto(b) File "/home/.conda/envs/bioembed1/lib/python3.7/http/client.py", line 509, in readinto n = self.fp.readinto(b) File "/home/.conda/envs/bioembed1/lib/python3.7/socket.py", line 589, in readinto return self._sock.recv_into(b) File "/home/.conda/envs/bioembed1/lib/python3.7/ssl.py", line 1071, in recv_into return self.read(nbytes, buffer) File "/home/.conda/envs/bioembed1/lib/python3.7/ssl.py", line 929, in read return self._sslobj.read(len, buffer) socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper status = run_func(*args) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper return func(self, options, args) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 378, in run reqs, check_supported_wheels=not options.target_dir File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve collected.requirements, max_rounds=limit_how_complex_resolution_can_be File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve state = resolution.resolve(requirements, max_rounds=max_rounds) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 427, in resolve failure_causes = self._attempt_to_pin_criterion(name) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 239, in _attempt_to_pin_criterion criteria = self._get_updated_criteria(candidate) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 230, in _get_updated_criteria self._add_to_criteria(criteria, requirement, parent=candidate) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria if not criterion.candidates: File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in bool return bool(self._sequence) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in bool return any(self) File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in
return (c for c in iterator if id(c) not in self._incompatible_ids)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
candidate = func()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 183, in _make_candidate_from_link
link, template, name, version
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link
version=version,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 296, in init
version=version,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in init
self.dist = self._prepare()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare
dist = self._prepare_distribution()
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 519, in prepare_linked_requirement
metadata_dist = self._fetch_metadata_only(req)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 372, in _fetch_metadata_only
req
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 394, in _fetch_metadata_using_link_data_attr
hashes=metadata_link.as_hashes(),
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 109, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/network/download.py", line 147, in call
for chunk in chunks:
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_internal/network/utils.py", line 87, in response_chunks
decode_content=False,
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 587, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/home/.conda/envs/bioembed1/lib/python3.7/contextlib.py", line 130, in exit
self.gen.throw(type, value, traceback)
File "/home/.conda/envs/bioembed1/lib/python3.7/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.