Open ParkMiSo opened 2 years ago
fkcoolman
commented
2 years ago I suggest you create a new conda environment with R env included when creating cpdb, something like this: conda create -n cpdb python=3.7 r-base and after you pip install cpdb, use conda to install ggplot2.
Romaindonne
commented
2 years ago Hello,
I am also trying to run cellphonedb plot dot_plot ... (from the tutorial files. I obtained the "out's files" with cellphonedb method statistical_analysis test_meta.txt test_counts.txt).
I am facing this error (very similar):
[ ][APP][25/04/22-22:12:55][ERROR] Unexpected error
Traceback (most recent call last):
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/api_endpoints/terminal_api/plot_terminal_api_endpoints/plot_terminal_commands.py", line 33, in dot_plot
r_plotter.dot_plot(means_path=means_path,
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/plotters/r_plotter.py", line 36, in wrapper
from rpy2 import robjects
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/rpy2/robjects/init.py", line 26, in
I have tried all the issues found there and always the same error. Miniconda3, python3.7, environment.yml, + conda + pip install cellphonedb
Could you help me with that?
Thanks a lot!
SinhaI
commented
2 years ago Hi,
I also got the same import error as above.
ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/proj/cellphone_env2/lib/python3.7/site-packages/markupsafe/__init__.py)
I was using markupsafe2.1.1. Downgrading markupsafe module to 2.0.1 cellphonedb plot worked fine for me.
I have used pip install markupsafe==2.0.1
Hope this will help.
Hi! I'm trying to plot the results of a cellphonedb and i have an error.
I'm using cellphonedb 2.1.7, R 4.0.5, and python 3.7.10. ggplot2 and phatmap installed.
I think that error is caused by setting the wrong R path. cpdb was in /data1/software/anaconda3/envs/cpdb/, but running R was in /opt/R/4.0.5/lib/R/. How can i resolve this issue?
This error was also caused using test data (cellphonedb example running)
The full message that return is :
/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.cluster.kmeans module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API. warnings.warn(message, FutureWarning) R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.0.5/lib/R/library/methods/libs/methods.so': /opt/R/4.0.5/lib/R/library/methods/libs/methods.so: undefined symbol: R_withCallingErrorHandler
R[write to console]: Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so': /opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: Rf_translateCharFP
R[write to console]: Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so': /opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: Rf_translateCharFP
R[write to console]: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so': /opt/R/4.0.5/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: Rf_translateCharFP
R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.0.5/lib/R/library/methods/libs/methods.so': /opt/R/4.0.5/lib/R/library/methods/libs/methods.so: undefined symbol: R_withCallingErrorHandler
R[write to console]: During startup - R[write to console]: Warning messages:
R[write to console]: 1: package "methods" in options("defaultPackages") was not found
R[write to console]: 2: package ‘grDevices’ in options("defaultPackages") was not found
R[write to console]: 3: package ‘graphics’ in options("defaultPackages") was not found
R[write to console]: 4: package ‘stats’ in options("defaultPackages") was not found
R[write to console]: 5: package ‘methods’ in options("defaultPackages") was not found
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/opt/R/4.0.5/lib/R/library/methods/libs/methods.so': /opt/R/4.0.5/lib/R/library/methods/libs/methods.so: undefined symbol: R_withCallingErrorHandler
[ ][APP][17/02/22-17:33:43][ERROR] Unexpected error Traceback (most recent call last): File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/plot_terminal_api_endpoints/plot_terminal_commands.py", line 38, in dot_plot columns=columns) File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/plotters/r_plotter.py", line 36, in wrapper from rpy2 import robjects File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/rpy2/robjects/init.py", line 17, in
from rpy2.robjects.robject import RObjectMixin, RObject
File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/rpy2/robjects/robject.py", line 58, in
class RObjectMixin(object):
File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/rpy2/robjects/robject.py", line 70, in RObjectMixin
__show = _get_exported_value('methods', 'show')
File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/rpy2/rinterfacelib/conversion.py", line 28, in
cdata = function(*args, **kwargs)
File "/data1/software/anaconda3/envs/cpdb/lib/python3.7/site-packages/rpy2/rinterface.py", line 773, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/R/4.0.5/lib/R/library/methods/libs/methods.so':
/opt/R/4.0.5/lib/R/library/methods/libs/methods.so: undefined symbol: R_withCallingErrorHandler