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Can not install compass #119

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wuxiangning opened this issue Nov 19, 2024 · 1 comment
Open

Can not install compass #119

wuxiangning opened this issue Nov 19, 2024 · 1 comment

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@wuxiangning
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Hello, after I installed and configured CPLEX, I proceeded to install Compass, but I encountered this error. However, my Visual Studio is able to configure C++ files normally. It seems that the issue is caused by my file path, but I’m not sure how to resolve it.Help!
my code:
git clone https://github.com/yoseflab/Compass.git
cd Compass
python setup.py install

the major error:
error: command 'E:\Ana\envs\cplex\Library\bin\cmake.exe' failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for python-libsbml
Running setup.py clean for python-libsbml
Successfully built compass-sc
Failed to build python-libsbml
ERROR: Could not build wheels for python-libsbml, which is required to install pyproject.toml-based projects

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@wuxiangning
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conda list compass

packages in environment at E:\Ana\envs\cplex:

Name Version Build Channel

compass-sc 0.9.10.2 pypi_0 pypi

compass -h
Traceback (most recent call last):
File "\?\E:\Ana\envs\cplex\Scripts\compass-script.py", line 33, in
sys.exit(load_entry_point('compass-sc==0.9.10.2', 'console_scripts', 'compass')())
File "\?\E:\Ana\envs\cplex\Scripts\compass-script.py", line 25, in importlib_load_entry_point
return next(matches).load()
File "E:\Ana\envs\cplex\lib\site-packages\importlib_metadata_init_.py", line 209, in load
module = import_module(match.group('module'))
File "E:\Ana\envs\cplex\lib\importlib_init_.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in load_unlocked
File "", line 728, in exec_module
File "", line 219, in call_with_frames_removed
File "E:\Ana\envs\cplex\lib\site-packages\compass_sc-0.9.10.2-py3.7.egg\compass\main.py", line 21, in
from .compass import cache
File "E:\Ana\envs\cplex\lib\site-packages\compass_sc-0.9.10.2-py3.7.egg\compass\compass_init
.py", line 3, in
from .algorithm import *
File "E:\Ana\envs\cplex\lib\site-packages\compass_sc-0.9.10.2-py3.7.egg\compass\compass\algorithm.py", line 14, in
from .. import utils
File "E:\Ana\envs\cplex\lib\site-packages\compass_sc-0.9.10.2-py3.7.egg\compass\utils.py", line 14, in
import anndata
File "E:\Ana\envs\cplex\lib\site-packages\anndata-0.11.1-py3.7.egg\anndata_init
.py", line 29, in
from ._core.anndata import AnnData
File "E:\Ana\envs\cplex\lib\site-packages\anndata-0.11.1-py3.7.egg\anndata_core\anndata.py", line 25, in
from .. import utils
File "E:\Ana\envs\cplex\lib\site-packages\anndata-0.11.1-py3.7.egg\anndata\utils.py", line 424
if new_path := deprecated_mapping.get(attr_name):
^
SyntaxError: invalid syntax

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