I am trying to run python as rmarkdwon code chunks. I was successful but rmarkdown by default uses Python2 and I want it to use Python 3. I am running it on Ubuntu with Python 2.7.6 installed and I installed anaconda with Python 3.5, which is the one I want rmarkdown use.
Here is the code and output of the python chunk in rmarkdown
import sys
print (sys.version)
and the output:
2.7.6 (default, Jun 22 2015, 17:58:13)
Any ideas?
You can add engine.path = '/path/to/python3' to override the python (2) executable. For example,
---
title: "python"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{python}
import sys
print(sys.version)
```
```{python, engine.path = '/usr/bin/python3'}
import sys
print(sys.version)
```
which python3. Whatever that returns is what you should use for engine.path.which python3?{python, engine.path = '~/home/user1/anaconda3/bin/python3'}. Still have the same error. Also tried {python, engine.path = '~/user1/anaconda3/bin/python3'} whit no success./home/user1/anaconda3/bin/python3. Currently you are entering ~/home/user1/anaconda3/bin/python3, which is presumably expanding to /home/user1/home/user1/anaconda3/bin/python.You can select your desired python version, as default, with an R chunk:
```{r setup, echo=FALSE}
library(knitr)
opts_chunk$set(engine.path = '/usr/bin/python3')
```
From now on your python chunks will use Python3:
```{python}
import sys
print(sys.version)
```
This way to select python version avoids to add the engine.path variable to every code chunk.
opts_chunk like this nor editing my .Rprofile to add Sys.setenv(PATH = paste("<path_to_python3>", Sys.getenv("PATH"), sep=":")) has set the default python correctly. I have no trouble setting an individual chunk to run python3 by setting the engine.path for that chunk, but setting all chunks to default to python3 hasn't worked; it still defaults to python2. I'm on version 1.1.423 of RStudio for Mac and R version 3.3.3. Would love to hear any suggestions!Actually, if you are running Python 3.x, which I am, I had to do the following (obviously your path to the Python3 executable might be different):
```{r Setup, echo=FALSE}
library(knitr)
opts_chunk$set('python', engine.path='/usr/local/Cellar/python3/3.6.3/bin/python3')
```
And could then create a chunk using just python and it would run in the correct version:
```{python, cache=TRUE, echo = FALSE, eval = TRUE}
import sys
print(sys.version)
```
You can use the reticulate package and insert an R chunk at the beginning:
```{r}
library(reticulate)
use_python("/usr/local/bin/python3")
```
