I removed my .emacs and .emacs.d, then created a new .emacs consisting of only the essential to use R and a shell with org-babel to make sure my configs weren't causing this:

(require 'org-install)
   (sh . t)
   (R . t)

When I try to run the following snippet:

#+begin_src R :results output verbatim
(any R code)

It runs just fine. However, if I add :session or :session name to the #+begin_src header, Emacs freezes. I can't move the cursor nor do anything. I can see both R and Emacs on htop, none using any CPU. The only way to get out is to send SIGTERM to Emacs.

When running the snippet with C-c the minibuffer says:

ESS (*R*, R (newest)) starting data directory? pwd (I say yes)
Cannot read history file pwd/.Rhistory

This is normal, I get it on other computers where Emacs doesn't freeze. Then hangs forever on

ess-tracebug mode enabled

Also normal. Except the hanging forever part.

A similar issue occurs with sh snippets:

#+begin_src sh :results output verbatim

Works fine. So with :session. However, with :session name it hangs forever just like R. All the minibuffer says is

Wrote /tmp/babel-XXXXX

And then hangs forever on

executing sh code block...

All packages (emacs, ess, org-mode) are the latest version from Debian stable repos. I have other computers with the same setup that work just fine. emacs --version returns GNU Emacs 24.4.1. The same happened in previous versions, and I also tried downloading Emacs 24.5.1 from a GNU mirror and compiling it. The exact same thing happens. I'm completely lost as to what could be causing this.


Also tried downloading latest stable ess and org-mode from the respective websites and installing and configuring for the compiled emacs. Added

(add-to-list 'load-path "/path/to/emacs-24.5/b/share/emacs/site-lisp/ess")
(load "ess-site") 

To .emacs as per ess' README

  • A bug report like this might have better luck on the Org mailing list than on this general emacs SE site.
    – mankoff
    Commented Jan 21, 2016 at 14:05

1 Answer 1

mv ~/.Rprofile{,.bak}
mv .RData{,bak}

I think the issue is a nonstandard options('prompt'). I (re)moved ~/.Rpofile and the .RData file for the working directory of the session and no longer had the blocking/endless waiting/frozen issue.

prompt as an issue also showed up when octave's default prompt changed: https://stackoverflow.com/questions/27742075/emacs-freezes-when-running-an-octave-code-block-within-org-mode

setting my prompt is now pretty complicated

.First <- function(...){
    updatePrompt <- function(...) {
      # Emacs Speaks Stats, use default prompt
           options(prompt="> "); 
      # Rstudio -- time but no colors
      else if( any(grepl("RStudio", .libPaths())) )
           options(prompt=format(Sys.time(), "\n# %X\n#> "))
      # command line R
                            "\n\e[38;5;197m# \e[38;5;27m%X\e[0;0m\n "))

    # add prompt if we're in interactive mode
    if(interactive()) { 


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