Importing matplotlib with reticulate in R

Question

I just started using the reticulate package in R, and I'm still getting a few of the kinks figured out. In particular, importing matplotlib is not going well. I've tried it two different ways, with different error messages for each.

First, using repl_python in RStudio's interactive shell:

library(reticulate)
use_python('/home/craig/anaconda3/bin/python')
py_discover_config()
repl_python()
import matplotlib.pyplot as plt

The REPL Python shell that opens up seems to have the correct version and everything, but when I try to import matplotlib.pyplot, I see the following:

ImportError: /lib/x86_64-linux-gnu/libz.so.1: version `ZLIB_1.2.9' not found (required by /home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/../../.././libpng16.so.16)

Installing zlib (using sudo apt-get install lib64z1-dev lib64z1) didn't seem to change anything. FWIW, import matplotlib worked just fine, as long as I don't need pyplot.

I also tried doing the same thing in an R Markdown document:

```{r}
library(reticulate)
py_discover_config()
```

```{python}
import matplotlib.pyplot as plt
```

This time I saw:

Error in py_get_attr_impl(x, name, silent): AtributeError: module 'matplotlib' has no attribute 'pyplot' Calls: ... $.python.builtin.object -> py_get_attr -> py_get_attr_impl -> .Call Execution halted

Any ideas what might be going on here?

Thanks!

UPDATE: As I mentioned in the comments, installing the developer version of reticulate fixes some of the problems, but not all. If I try to run this Rmd:

```{r}
library(reticulate)
use_python('/home/craig/anaconda3/bin/python')
```

```{python}
import matplotlib.pyplot as plt
```

I get the following error messages:

Error in py_run_string_impl(code, local, convert) : 
  ImportError: /home/craig/anaconda3/lib/python3.6/site-packages/PyQt5/../../../libxcb-dri3.so.0: undefined symbol: xcb_send_request_with_fds

Detailed traceback: 
  File "<string>", line 1, in <module>
  File "/home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py", line 116, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 60, in pylab_setup
[backend_name], 0)
  File "/home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py", line 16, in <module>
    from .backend_qt5 import (
  File "/home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_qt5.py", line 18, in <module>
    import matplotlib.backends.qt_editor.figureoptions as figureoptions
  File "/home/craig/anaconda3/lib/python3.6/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
Calls: <Anonymous> ... force -> py_run_string -> py_run_string_impl -> .Call
Execution halted

When I tried googling the error text, a similar error with xcb does seem to be coming up in a context that is, as far as I can tell, not so relevant.

Answer 1

I was able to get things working by changing the R Markdown code block to read:

```{r}
library(reticulate)
use_python('/usr/bin/python3')
```

```{python}
import matplotlib.pyplot as plt
```

I still don't really understand why, but it seems that reticulate doesn't play nice with anaconda installations. Maybe it has something to do with anaconda being set up to work well with an interactive Jupyter notebook.