Reticulate - Running python chunks in Rmarkdown

You must use the Rstudio daily build (source) and upgrade knitr, rmarkdown to the latest version.

> packageVersion("rmarkdown")
[1] ‘1.9’
> packageVersion("knitr")
[1] ‘1.20’

Rmarkdown / knitr:

Running the chunks:

Running the chunks without knitting the document is not supported so far. See here: https://github.com/yihui/knitr/issues/1440 or Reticulate not sharing state between R/Python cells or Python/Python cells in RMarkdown.

Edit: Workaround by Freguglia:

"Workaround is to turn python chunks into R chunks and just wrap the whole content in the py_run_string() function, so whatever you assign in that piece of code is accessible from R by py$variable_name."

Knitting the document:

One way is to upgrade knitr as suggested above, but you dont have to and you also dont need RStudio daily build.

If you have a version of knitr prior to 1.18, you can include:

```{r setup, include = FALSE} knitr::knit_engines$set(python = reticulate::eng_python) ``` , see here: https://rstudio.github.io/reticulate/articles/r_markdown.html#engine-setup.

Python:

If it doesnt work ensure the python connection is running outside of rmarmdown/knitr: py_run_string("x = 10"); py$x.

In case that also doesnt work, you should check: py_available() and py_numpy_available().

If it returns FALSE: Try to initialize it with: py_available(TRUE).

If that´s still a no - check your config: py_config()

It will give you further hints on the problem:

Examples for me were: different bit versions of R and python (32 vs 64) or somehow i ran into trouble having installed both Python2.7 and seperately Anaconda.