Open queirozhanna opened 2 months ago
coolmaksat
commented
2 months ago Hi, Which version of python are you using? Please use python3.7. I don't see word2vec requirement in https://github.com/bio-ontology-research-group/deepgoplus/blob/master/requirements.txt. I would recommend installing the dependencies with pip
remkv6
commented
5 days ago I created a tutorial for deepgoplus that shows how I installed and ran the software here. Perhaps it will be helpful https://bioinformaticsworkbook.org/dataAnalysis/GenomeAnnotation/DeepGoPlus_AI_Functional_Prediction_of_Proteins.html#gsc.tab=0
coolmaksat
commented
4 days ago Thank you. Great work!
Hi!
I've installed the majority of the required packages, but I'm facing errors installing word2vec. I've tried "conda install word2vec==0.10.2", "pip install word2vec==0.10.2" and "python3 -m pip install word2vec==0.10.2" but neither of these work.
When I try to install by conda, I receive this message: `$ conda install word2vec==0.10.2 Channels:
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.`
and when I try to install by pip install or python3 - m pip install, I receive this: `pip install word2vec==0.10.2 Defaulting to user installation because normal site-packages is not writeable Collecting word2vec==0.10.2 Using cached word2vec-0.10.2.tar.gz (60 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [43 lines of output] Traceback (most recent call last): File "", line 2, in
File "", line 34, in
File "/tmp/pip-install-o6469j0x/word2vec_6a08e0e29b6e402db3c30ef993ccb849/setup.py", line 102, in
ext_modules=cythonize("word2vec/word2vec_noop.pyx"),
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1008, in cythonize
ctx = Context.from_options(c_options)
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/Main.py", line 100, in from_options
return cls(options.include_path, options.compiler_directives,
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/Main.py", line 78, in init
from . import Builtin, CythonScope
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/CythonScope.py", line 5, in
from .UtilityCode import CythonUtilityCode
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/UtilityCode.py", line 3, in
from .TreeFragment import parse_from_strings, StringParseContext
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/TreeFragment.py", line 17, in
from .Visitor import VisitorTransform
File "Cython/Compiler/Visitor.py", line 16, in init Cython.Compiler.Visitor
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/Nodes.py", line 33, in
from .Pythran import has_np_pythran, pythran_type, is_pythran_buffer
File "/home/queirozhanna/.local/lib/python3.10/site-packages/Cython/Compiler/Pythran.py", line 10, in
import pythran
File "/usr/lib/python3/dist-packages/pythran/init.py", line 41, in
from pythran.toolchain import (generate_cxx, compile_cxxfile, compile_cxxcode,
File "/usr/lib/python3/dist-packages/pythran/toolchain.py", line 6, in
from pythran.backend import Cxx, Python
File "/usr/lib/python3/dist-packages/pythran/backend.py", line 7, in
from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
File "/usr/lib/python3/dist-packages/pythran/analyses/init.py", line 12, in
from .aliases import Aliases, StrictAliases
File "/usr/lib/python3/dist-packages/pythran/analyses/aliases.py", line 6, in
from pythran.syntax import PythranSyntaxError
File "/usr/lib/python3/dist-packages/pythran/syntax.py", line 7, in
from pythran.tables import MODULES
File "/usr/lib/python3/dist-packages/pythran/tables.py", line 174, in
BINARY_UFUNC = {"accumulate": FunctionIntr()}
File "/usr/lib/python3/dist-packages/pythran/intrinsic.py", line 101, in init
super(FunctionIntr, self).init(**kwargs)
File "/usr/lib/python3/dist-packages/pythran/intrinsic.py", line 58, in init
self.args = ast.arguments(
File "/home/queirozhanna/.local/lib/python3.10/site-packages/gast/gast.py", line 10, in create_node
assert nbparam in (0, len(Fields)), \
AssertionError: Bad argument number for arguments: 7, expecting 6
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.`
Without word2vec==0.10.2, I can't install DeepGOPlus, which is necessary to my work 😔