cellphonedb plot issue

[ParkMiSo]

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.k_means_ 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/rinterface_lib/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

[fkcoolman]

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]

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
from . import vectors
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/rpy2/robjects/vectors.py", line 14, in
import jinja2 # type: ignore
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/jinja2/init.py", line 12, in
from .environment import Environment
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/jinja2/environment.py", line 25, in
from .defaults import BLOCK_END_STRING
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/jinja2/defaults.py", line 3, in
from .filters import FILTERS as DEFAULT_FILTERS # noqa: F401
File "/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/jinja2/filters.py", line 13, in
from markupsafe import soft_unicode
ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/opt/anaconda3/envs/cpdb/lib/python3.8/site-packages/markupsafe/init.py)

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]

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.