Knit error when using reticulate in Rmarkdown

[Alalalalaki]

Hi

This is related to #831 . I face up to exactly the same error and by using development version of reticulate, I can now successfully run python chunks directly in Rmarkdown. However, when I knit the Rmarkdown, it stops at $ engine: chr "python" and never finish running or report any errors.

Thanks.

[kevinushey]

Without a reproducible example, there is nothing I can do.

[Alalalalaki]

@kevinushey Sorry, I thought this is trivial.

[mabesa]

Hi, I encounter the same behaviour. Already spent hours trying to get my doc knit to html and would really appreciate a hint for a search direction.

This is my markdown example which works as expected when "Run All" but stalls at $ engine: chr "python" (- before ``` added to be able to display the markdown file). Also tried to ask on stack exchange but wasn't able to solve the problem so far.

---
title: "test knitr python"
output: html_document
---

-```{r setup, include=FALSE}
library(reticulate)
use_python('~/anaconda3/envs/gwpy37/bin/python3')
knitr::opts_chunk$set(echo = TRUE)
-```

-```{r}
version$version.string
rstudioapi::versionInfo()$version
packageVersion('reticulate')
-```

[1] "R version 4.0.2 (2020-06-22)"
[1] ‘1.3.959’
[1] ‘1.18.9000’

-```{python}
import sys
sys.version

a = 1
-```

'3.7.9 (default, Aug 31 2020, 07:24:53) \n[Clang 10.0.0 ]'

-```{r}
py$a
-```

[1] 1

[mabesa]

Was able to knit the minimal example above by specifying knitr::opts_chunk$set(engine.path = list(python = '/Library/Frameworks/Python.framework/Versions/3.8/bin/python3')) in the setup chunk. Could this be an issue with anaconda? I cannot knit when I try to use the python 3.8 version in anaconda in ~/anaconda3/envs/gwpy38/bin/python in the opts_chunk command.

[JohnGranger]

You can render Rmd file in console, like this:

> rmarkdown::render("test.Rmd")