Importing rpy2.robjects fails with R>=4.2

[scottgigante-immunai]

Describe the issue or bug

rpy2 cannot be imported if the R version is >=4.2

To Reproduce

import rpy2.robjects

Error

Error in .makeMessage(..., domain = domain) : 
  3 arguments passed to .Internal(gettext) which requires 2
Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 19, in <module>
    import rpy2.robjects.functions
  File "/opt/hostedtoolcache/Python/3.7.12/x[64](https://github.com/scottgigante-immunai/scprep/runs/6183376716?check_suite_focus=true#step:4:64)/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 11, in <module>
    from rpy2.robjects import help
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/help.py", line 45, in <module>
    quiet_require('tools')
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/help.py", line 41, in quiet_require
    ok = _eval(expr)
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
    cdata = function(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface.py", line 810, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2

Additional context
Example Github Actions workflow reproducing the error is here: https://github.com/scottgigante-immunai/scprep/actions/runs/2229334197/workflow

[lgautier]

rpy2's test matrix has R-4.2.0 (for example, see https://github.com/rpy2/rpy2/runs/6141867886?check_suite_focus=true) and it appears that it installs and passes all automated tests.

The error message observed might be caused by the R environment setup not telling the linker where to find the R shared library. The rpy2 tests suite ensures that this is the case:
https://github.com/rpy2/rpy2/blob/master/.github/workflows/pythonpackage.yml

I am closing this as resolved. Reopen if the diagnosis is incorrect.

[scottgigante-immunai]

Okay, I figured it out. In order for rpy2 to work on Actions with R >= 4.2, you need to

• use actions/setup-python@v1 (NOT actions/setup-python@v2)
• Set LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}

Example here: https://github.com/scottgigante-immunai/scprep/runs/6241490722?check_suite_focus=true

[vnijs]

@scottgigante-immunai I'm having a similar issue with rpy2, installed using conda, and rpy2 (see below). Can you provide a bit more detail perhaps on how you got this working? Thanks

❯ export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
❯ python -c 'from rpy2.robjects import r'

Error in .makeMessage(..., domain = domain) : 
  3 arguments passed to .Internal(gettext) which requires 2
Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/conda/lib/python3.9/site-packages/rpy2/robjects/__init__.py", line 19, in <module>
    import rpy2.robjects.functions
  File "/opt/conda/lib/python3.9/site-packages/rpy2/robjects/functions.py", line 11, in <module>
    from rpy2.robjects import help
  File "/opt/conda/lib/python3.9/site-packages/rpy2/robjects/help.py", line 45, in <module>
    quiet_require('tools')
  File "/opt/conda/lib/python3.9/site-packages/rpy2/robjects/help.py", line 41, in quiet_require
    ok = _eval(expr)
  File "/opt/conda/lib/python3.9/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
    cdata = function(*args, **kwargs)
  File "/opt/conda/lib/python3.9/site-packages/rpy2/rinterface.py", line 810, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2

❯ python -m rpy2.situation

rpy2 version:
3.5.1
Python version:
3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:51:20) 
[GCC 10.3.0]
Looking for R's HOME:
    Environment variable R_HOME: /usr/local/lib/R
    Calling `R RHOME`: /usr/local/lib/R
    Environment variable R_LIBS_USER: None
R's additions to LD_LIBRARY_PATH:
/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-11-openjdk-arm64/lib/server
R version:
    In the PATH: R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
    Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
  include:
  ['/usr/local/lib/R/include']
  libraries:
  ['R', 'pcre2-8', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'iconv', 'icuuc', 'icui18n']
  library_dirs:
  ['/usr/local/lib', '/usr/local/lib/R/lib']
  extra_compile_args:
  []
  extra_link_args:
  ['-Wl,--export-dynamic', '-fopenmp']

[scottgigante-immunai]

@vnijs unfortunately I don't know what actually fixed it. But since setup-python v2 breaks and v1 works, whatever actually fixed it is located in this diff

[vnijs]

@scottgigante-immunai Not sure I follow. Do you have rpy2 working with R 4.2? If so, what did you do in addition to the below?

LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}

[scottgigante-immunai]

I'm running on Github Actions, and in addition to the LD_LIBRARY_PATH step above, I used a different Python install (actions/setup-python@v1 rather than actions/setup-python@v2). There are quite a few differences between those two, and unfortunately I don't know which one made the difference; I just know that v1 works and v2 doesn't.

[vnijs]

@lgautier Would you consider re-opening this issue? It seems there is an issue with rpy2 and R2.4, at least as it relates a specific form of python set up #876

[vnijs]

@lgautier I could use your help to see how to resolve this issue. To get a reproducible example, please run the below. Sorry, the image is large.

docker run --rm -p 8989:8989 vnijs/rsm-jupyter:2.4.0

JupyterLab will be available at the link below:

http://localhost:8989/lab

You will see a popup with the message "JupyterLab Code Formatter Error". The issue linked below describes the problem with rpy2 and R 4.2.0

ryantam626/jupyterlab_code_formatter#258

In jupyterlab you can directly see the problem by using from rpy2.robjects import r

Note that we have been using rpy2 with this docker image design for some time and it works great with R 4.1.2. See below.

docker run --rm -p 8989:8989 vnijs/rsm-jupyter:2.3.0

I would appreciate any guidance you can provide. Thanks

-- Vincent

[lgautier]

@scottgigante-immunai - This might have been an issue with actions/setup-python@v2. Python 3.10 and R-4.2 appears to be working fine when using v2 now:
#876

[vnijs]

@lgautier FYI The issue we are having with rpy2 is with Python 3.9.12 (conda) and R 4.2.0 installed from source. Both R and Python work fine.

[scottgigante-immunai]

@lgautier can confirm this is fixed with v1, v2, v3, whether or not we set LD_LIBRARY_PATH. Config here: https://github.com/scottgigante-immunai/scprep/actions/runs/2404691023

[GegznaV]

Similar issue:
https://stackoverflow.com/questions/74420263/ipynb-load-ext-rpy2-ipython-errors-3-arguments-passed-to-internalgette
Could you, please, add your comment on Stack Overflow?

[brainfo]

Similar issue: https://stackoverflow.com/questions/74420263/ipynb-load-ext-rpy2-ipython-errors-3-arguments-passed-to-internalgette Could you, please, add your comment on Stack Overflow?

same here: from rpy2.robjects import help

But I found it only in jupyter lab. With python script in the same env, it works fine.

File /mnt/data/hong/anaconda3/envs/scanpy/lib/python3.9/site-packages/rpy2/robjects/help.py:41, in quiet_require(name, lib_loc)
     38 expr_txt = ('suppressPackageStartupMessages(base::require(%s, lib.loc=%s))'
     39             % (name, lib_loc))
     40 expr = rinterface.parse(expr_txt)
---> 41 ok = _eval(expr)
     42 return ok

File /mnt/data/hong/anaconda3/envs/scanpy/lib/python3.9/site-packages/rpy2/rinterface_lib/conversion.py:45, in _cdata_res_to_rinterface.<locals>._(*args, **kwargs)
     44 def _(*args, **kwargs):
---> 45     cdata = function(*args, **kwargs)
     46     # TODO: test cdata is of the expected CType
     47     return _cdata_to_rinterface(cdata)

File /mnt/data/hong/anaconda3/envs/scanpy/lib/python3.9/site-packages/rpy2/rinterface.py:817, in SexpClosure.__call__(self, *args, **kwargs)
    810     res = rmemory.protect(
    811         openrlib.rlib.R_tryEval(
    812             call_r,
    813             call_context.__sexp__._cdata,
    814             error_occured)
    815     )
    816     if error_occured[0]:
--> 817         raise embedded.RRuntimeError(_rinterface._geterrmessage())
    818 return res

RRuntimeError: Error in gettext(fmt, domain = domain, trim = trim) : 
  3 arguments passed to .Internal(gettext) which requires 2

[phantom-duck]

@GegznaV The issue in stackoverflow you linked to seems very similar to the one I had. In my case, defining an environmental variable R_HOME to the home folder of the R installation seems to have worked.

e.g. in PowerShell: $env:R_HOME = 'C:\Program Files\R\R-4.2.2'

A link that proved a bit helpful: https://rpy2.github.io/doc/v3.5.x/html/rinterface.html#module-rpy2.rinterface

Specifically, the part about rpy2.rinterface.initr has a note which was the only place I found that mentioned something along the lines of the problem we seem to be facing here.

[RichardScottOZ]

That did seem to stop the error

Could this be related to R installed for system and things installed for user? e.g. AppData etc.

[phantom-duck]

In my case, I believe that it had to do with the R executable not having been added to my PATH environmental variable. Possibly because I did not allow it during installation of R, but I do not remember. So, if, for example, I open up a terminal and try to invoke an R executable, e.g. Rscript, it does not work, it cannot find it. And most probably the same goes for my rpy2 library, it failed to find the executable of R. and that is why I needed to provide it with the R_HOME variable.

Of course, I do not know if this applies to your case as well.

[ramdhanhdy]

@GegznaV The issue in stackoverflow you linked to seems very similar to the one I had. In my case, defining an environmental variable R_HOME to the home folder of the R installation seems to have worked.

e.g. in PowerShell: $env:R_HOME = 'C:\Program Files\R\R-4.2.2'

A link that proved a bit helpful: https://rpy2.github.io/doc/v3.5.x/html/rinterface.html#module-rpy2.rinterface

Specifically, the part about rpy2.rinterface.initr has a note which was the only place I found that mentioned something along the lines of the problem we seem to be facing here.

I still get the same error

[EngrStudent]

Okay, I figured it out. In order for rpy2 to work on Actions with R >= 4.2, you need to

• use actions/setup-python@v1 (NOT actions/setup-python@v2)
• Set LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}

Example here: https://github.com/scottgigante-immunai/scprep/runs/6241490722?check_suite_focus=true

Actions for this link have expired and are no longer available.

[lgautier]

FWIW rpy2's own Actions use setup-python@v4 (https://github.com/rpy2/rpy2/actions/runs/5631973670/job/15259461468#step:3:1) and R is 4.3 (https://github.com/rpy2/rpy2/actions/runs/5631973670/job/15259461468#step:4:1100).