I am trying to run a R Markdown document which uses both R and Python code chunks. I am on macOS Catalina version 10.15.2, R version is 3.6.2 and RStudio version is 1.2.5033. I am using the reticulate package version 1.14.
which python on the Terminal reveals /Users/dhirajkhanna/opt/anaconda3/bin/python and the same is entered in my .Renviron file as RETICULATE_PYTHON=/Users/dhirajkhanna/opt/anaconda3/bin/python. Strangely when I do Sys.which('python') in my RStudio console, it shows me a different path, viz. /usr/bin/python. When I load the reticulate package, the output of py_config() is:
python: /usr/local/bin/python3
libpython: /usr/local/opt/python/Frameworks/Python.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7.dylib
pythonhome: /usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7:/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7
version: 3.7.4 (default, Jul 9 2019, 18:13:23) [Clang 10.0.1 (clang-1001.0.46.4)]
numpy: /usr/local/lib/python3.7/site-packages/numpy
numpy_version: 1.16.4
python versions found:
/usr/bin/python3
/usr/local/bin/python3
/usr/bin/python
/usr/local/bin/python
/Users/dhirajkhanna/anaconda3/bin/python
/Users/dhirajkhanna/.virtualenvs/object_recognition_detection/bin/python
/Users/dhirajkhanna/.virtualenvs/object_recognition_detection1/bin/python
/Users/dhirajkhanna/.virtualenvs/r-tensorflow/bin/python
/Users/dhirajkhanna/venv/bin/python
If I specify, use_python('/Users/dhirajkhanna/opt/anaconda3/bin/python'), the output of py_config() is:
python: /Users/dhirajkhanna/opt/anaconda3/bin/python
libpython: /Users/dhirajkhanna/opt/anaconda3/lib/libpython3.7m.dylib
pythonhome: /Users/dhirajkhanna/opt/anaconda3:/Users/dhirajkhanna/opt/anaconda3
version: 3.7.5 (default, Oct 25 2019, 10:52:18) [Clang 4.0.1 (tags/RELEASE_401/final)]
numpy: /Users/dhirajkhanna/opt/anaconda3/lib/python3.7/site-packages/numpy
numpy_version: 1.17.3
python versions found:
/Users/dhirajkhanna/opt/anaconda3/bin/python
/usr/bin/python3
/usr/local/bin/python3
/usr/bin/python
/usr/local/bin/python
/Users/dhirajkhanna/anaconda3/bin/python
/Users/dhirajkhanna/.virtualenvs/object_recognition_detection/bin/python
/Users/dhirajkhanna/.virtualenvs/object_recognition_detection1/bin/python
/Users/dhirajkhanna/.virtualenvs/r-tensorflow/bin/python
/Users/dhirajkhanna/venv/bin/python
Now when I try to load Python packages in a Python code chunk, RStudio crashes:
import pandas as pd
import matplotlib.pyplot as plt
I get the "R Session Aborted" message. All this was working fine till I upgraded R. Any idea how to rectify this?
Edit
While trying this in R, I get a segmentation error:
> library(reticulate)
> repl_python()
Python 3.7.6 (/Users/dhirajkhanna/opt/anaconda3/bin/python)
Reticulate 1.14 REPL -- A Python interpreter in R.
>>> import pandas as pd
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: py_eval_impl(code, convert)
2: py_eval("_", convert = FALSE)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(py_eval("_", convert = FALSE), error = function(e) r_to_py(NULL))
7: py_last_value()
8: py_compile_eval(code)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(py_compile_eval(code), error = handle_error)
13: repl()
14: repl_python()
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
I have also tried running a different version of Python (3.6) in a virtualenv but still no joy.
A clean install of Rcpp and reticulate solved the problem. More details here.