fail to run plot

[teichlab]

fail to run plot

[mvento]

Hi @YiqunCao,

Thanks for using CellPhoneDB.
Some questions:

• What distro/version of Linux are you using?
• What Python/R versions are you using?
• What CellPhoneDB version are you using?
• What command are you trying to use?

Using plots requires R and some R libraries. Some people experiments compatibility errors. To avoid these errors, we highly recommend using CellPhoneDB Docker image.

Best

[djh1991]

Hi,
I get the same error as follows:
"""
[root@localhost example_data]# cellphonedb plot dot_plot
[ ][APP][21/10/19-08:06:36][ERROR] Unexpected error
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/cellphonedb/src/api_endpoints/terminal_api/plot_terminal_api_endpoints/plot_terminal_commands.py", line 38, in dot_plot
columns=columns)
File "/usr/local/lib/python3.6/site-packages/cellphonedb/src/plotters/r_plotter.py", line 35, in wrapper
from rpy2.rinterface_lib.embedded import RRuntimeError
File "/usr/local/lib/python3.6/site-packages/rpy2/rinterface_lib/embedded.py", line 7, in
from . import openrlib
File "/usr/local/lib/python3.6/site-packages/rpy2/rinterface_lib/openrlib.py", line 41, in
_get_dataptr_fallback)
File "/usr/local/lib/python3.6/site-packages/rpy2/rinterface_lib/openrlib.py", line 26, in _get_symbol_or_fallback
res = getattr(rlib, symbol)
RuntimeError: found a situation in which we try to build a type recursively. This is known to occur e.g. in ``struct s { void(*callable)(struct s); }''. Please report if you get this error and really need support for your case.
"""
R 3.6.1
python 3.6
system : centos 8
It can find the R and R librarires Correctly， but can not get the function by getattr。 Does it was a bug when run rpy2 in centos8?

[babiddy]

I helped someone in our lab who was running into the same error. We followed the advice from here, and ran this command pip install cffi==1.12.3 in the virtual environment that cellphonedb is installed in. This fixed the issue for us.

[mvento]

Hi @babiddy,

I very appreciate your help. We will add this library to Python requirements.

Best

[babiddy]

Hello @mvento!

I'm happy I could help. CellPhoneDB is a great tool and has been useful for us. Can't wait to see how it develops!

Best
Brent

[djh1991]

Hi @babiddy @mvento
Thank you for your advices。 I tried again and resolved this question.