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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.

Home Page:https://zhanghao-njmu.github.io/SCP/

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Error in py_module_import(module, convert = convert) : NameError: name 'base_events' is not defined

zoan128 opened this issue · comments

commented

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_and_load(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_and_load(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_and_load(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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(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_and_load(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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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_and_load(name, import)
File "C:\Users\Lenovo\AppData\Local\R-MINI1\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)
commented

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.

commented

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