seqVec installation Error

[amalislam675]

To install seqvec, I first install python=3.7.13 on new virtual environment then i install seqvec using pip install seqvec I am encountering this error, can you help to fix? 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 237, in _attempt_to_pin_criterion for candidate in criterion.candidates: 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.

[konstin]

This looks like either a random network error or something in your firewall being misconfigured, can you retry?

[amalislam675]

This looks like either a random network error or something in your firewall being misconfigured, can you retry?

I tried it two or three times, but I am always getting the same error.

[XinCao02]

I got a subprocess error for pip install seqvec, but I tried pip install seqvec --no-deps and succeeded. (I had bio-embeddings & torch==2.0.1 installed successfully before)