Environment variables and RStudio

I'm using RStudio and have been trying to use the rPython package to do some email handling for me. This involves unpacking some email attachments so I need to use a newer version of Python than 2.7.

I am on ubuntu so I've set environment variables in a bash script which I can see has worked:

bash

alias python=python3
export RPYTHON_PYTHON_VERSION=3

command line

echo $RPYTHON_PYTHON_VERSION
3

And yet, when I install rPython in RStudio it says:

Installing package into ‘/home/richardc/R/x86_64-pc-linux-gnu-library/3.1’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/rPython_0.0-5.tar.gz' Content type 'application/x-gzip' length 37109 bytes (36 Kb)

opened URL

downloaded 36 Kb

installing source package ‘rPython’ ... ** package ‘rPython’ successfully unpacked and MD5 sums checked a specific python version to use was not provided defaulting to the standard python in the system

So, despite python --version returning 3.4 and setting the environment variable it is defaulting to 2.7

I'm hoping that there is something straightforward I'm missing.

Solution

@nickbloom was actually close to it, but it is not Sys.setenv(RPYTHON_PYTHON_PATH=3) but Sys.setenv(RPYTHON_PYTHON_VERSION=3)

In my case (I have Python 3.5) it was:

> Sys.setenv(RPYTHON_PYTHON_VERSION=3.5)  
> install.packages('rPython')  
Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) trying URL  
'http://r.meteo.uni.wroc.pl/src/contrib/rPython_0.0-5.tar.gz' Content  
type 'application/x-gzip' length 37109 bytes (36 KB)  
================================================== downloaded 36 KB  

* installing *source* package ‘rPython’ ...  
** package ‘rPython’ successfully unpacked and MD5 sums checked which: no python3.5-config in (/sbin:/bin:/usr/sbin:/usr/bin) could not  
locate python3.5-config

As you can see now it is looking for python3.5-config, which is the version I specified above.

Also if your python3.5-config file is not in the PATH then you might also want to set the PATH:

Sys.setenv(PATH='/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/bin')

You might also need to rename python3.5m-config, because rPython always looks for [pythoncommand]-config, which in my case was python3.5 and not python3.5m, so I just renamed python3.5m-config to python3.5-config and then the rPython package has installed.