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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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Error in py_module_import(module, convert = convert) : NameError: name 'base_events' is not defined #172

Closed zoan128 closed 10 months ago

zoan128 commented 11 months ago

I encoutered an error when I do "ref_data <- srt_to_adata(ref)" and "ref" is a seuratobject.

**My code ：

prepare

if (!require("devtools", quietly = TRUE)) { install.packages("devtools") } devtools::install_github("zhanghao-njmu/SCP") SCP::PrepareEnv() library(SCP)

convert

ref <- readRDS("E:/ewdata/CRJdataanalysis/analysis/Chai_ref.rds")

ref_data <- srt_to_adata(ref)**

Error in py_module_import(module, convert = convert) : NameError: name 'base_events' is not defined Run `reticulate::py_last_error()` for details.

Reticulate::py_last_error() shows：

── Python Exception Message ───────────────────────────────────────────────────────────────────── Traceback (most recent call last): File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scanpy__init.py", line 14, in from . import tools as tl File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scanpy\tools__init.py", line 1, in from ..preprocessing import pca File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scanpy\preprocessing__init.py", line 1, in from ._recipes import recipe_zheng17, recipe_weinreb17, recipe_seurat File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scanpy\preprocessing_recipes.py", line 12, in from ._normalization import normalize_total File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scanpy\preprocessing_normalization.py", line 7, in from sklearn.utils import sparsefuncs File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\sklearn__init.py", line 82, in from .base import clone File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\sklearn\base.py", line 17, in from .utils import _IS_32BIT File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\sklearn\utils\init.py", line 29, in from .fixes import parse_version, threadpool_info File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\sklearn\utils\fixes.py", line 19, in import scipy.stats File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scipy\stats\init__.py", line 485, in from ._stats_py import * File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\scipy\stats_stats_py.py", line 37, in from numpy.testing import suppress_warnings File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\site-packages\numpy\testing\init__.py", line 8, in from unittest import TestCase File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\unittest\init.py", line 60, in from .async_case import IsolatedAsyncioTestCase File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\unittest\async_case.py", line 1, in import asyncio File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 119, in _find_and_load_hook return _run_hook(name, _hook) File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 93, in _run_hook module = hook() File "E:\R-4.3.1\library\reticulate\python\rpytools\loader.py", line 117, in _hook return _find_andload(name, import) File "C:\Users\Lenovo\AppData\Local\R-MINI~1\envs\SCP_env\lib\asyncio\init.py", line 26, in all__ = (base_events.all__ + NameError: name 'base_events' is not defined

── R Traceback ────────────────────────────────────────────────────────────────────────────────── ▆

  1. └─SCP::srt_to_adata(ref)
  2. └─reticulate::import("scanpy", convert = FALSE)
  3. └─reticulate:::py_module_import(module, convert = convert)
ZHOUDI0929 commented 10 months ago

pak::pak("rstudio/reticulate")

This problem caused by "reticulate". You can use pak update reticulate, and this issue should be solved.

As someone who doesn’t know python at all, python environment configuration took me a whole day. Fortunately, python and R are similar, otherwise I wouldn’t know how to solve those errors.

zhanghao-njmu commented 10 months ago

This issue is caused by reticulate. You need to install the development version of reticulate. https://community.rstudio.com/t/problem-with-tensorflow-2-10-and-rstudio/173917/4