I use Anaconda Jupyter notebook via VSCode or directly via browser.
I installed rpy2 via conda as:
conda install -c r r-essentials rpy2 --yes
Then in a Python cell of Jupyter Notebook, I ran:
%load_ext rpy2.ipython
And got
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) :
3 arguments passed to .Internal(gettext) which requires 2
Details
I use Windows 10. I have a separate R installation on my computer too.
In ipynb, the same error appears if I run:
import rpy2.robjects as robjects
More details on the error:
%load_ext rpy2.ipython
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) :
3 arguments passed to .Internal(gettext) which requires 2
Output exceeds the size limit. Open the full output data in a text editor
---------------------------------------------------------------------------
RRuntimeError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_18052\1837600852.py in <cell line: 1>()
----> 1 get_ipython().run_line_magic('load_ext', 'rpy2.ipython')
c:\Users\user\anaconda3\lib\site-packages\IPython\core\interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2415 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2416 with self.builtin_trap:
-> 2417 result = fn(*args, **kwargs)
2418 return result
2419
c:\Users\user\anaconda3\lib\site-packages\decorator.py in fun(*args, **kw)
230 if not kwsyntax:
231 args, kw = fix(args, kw, sig)
--> 232 return caller(func, *(extras + args), **kw)
233 fun.__name__ = func.__name__
234 fun.__doc__ = func.__doc__
c:\Users\user\anaconda3\lib\site-packages\IPython\core\magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
...
812
RRuntimeError: Error in gettext(fmt, domain = domain, trim = trim) :
3 arguments passed to .Internal(gettext) which requires 2
Other things I tried:
# Works:
import rpy2
print(rpy2.__version__)
# Returns:
3.5.1
import rpy2.situation
for row in rpy2.situation.iter_info():
print(row)
# Returns:
rpy2 version:
3.5.1
Python version:
3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:50:36) [MSC v.1929 64 bit (AMD64)]
Looking for R's HOME:
Environment variable R_HOME: None
InstallPath in the registry: C:\Program Files\R\R-4.2.2
Environment variable R_USER: None
Environment variable R_LIBS_USER: None
Unable to determine R library path: Command '('C:\\Users\\user\\anaconda3\\lib\\R\\bin\\Rscript', '-e', 'cat(Sys.getenv("LD_LIBRARY_PATH"))')' returned non-zero exit status 1.
R version:
In the PATH: R version 4.1.3 (2022-03-10) -- "One Push-Up"
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
['C:/PROGRA~1/R/R-4.2.2/include', 'C:/PROGRA~1/R/R-4.2.2/include/x64']
libraries:
['R', 'm']
library_dirs:
['C:/PROGRA~1/R/R-4.2.2/bin/x64']
extra_compile_args:
[]
extra_link_args:
[]
A similar issue with no answer is here.
Might be related but is related to continuous integration: https://github.com/rpy2/rpy2/issues/874
