YosefLab / Compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
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Can not install compass #119

Open wuxiangning opened 6 days ago

wuxiangning commented 6 days ago

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 commented 6 days ago

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