[O] R output with session polluted with ascii color codes

[Tyler Smith]

Hi,

The printed output of some R functions includes ascii color codes (i.e., 
). This causes problems with R code blocks evaluated with the :session 
option. I've pasted a file below that demonstrates the problem. (should I 
attach it as a file? not sure what's preferable).

I can't find a way to disable this feature from R. However, I did find a way to 
filter out these codes from the babel side. The function of interest is 
~org-babel-R-evaluate-session` in ob-R.el. Adding a ~(replace-regexp-in-string 
ansi-color-control-seq-regexp "" ...)~ form around the output strips away the 
color codes so they don't mess up the output.  I've included that code in the 
example. If that makes sense I can put that together as a patch. If that 
doesn't make sense, please let me know how to fix this!

Best,

Tyler

* Reproducible Example

Start with ~emacs -Q~, then evaluate each of the following code blocks
in turn.

#+BEGIN_SRC elisp setup
(require 'package)
(setq package-load-list
      '((org-plus-contrib t)
        (ess t)
        (julia-mode t)))
(package-initialize)
(require 'org)
(require 'ess)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (R . t)
   (shell . t)))
#+END_SRC

#+RESULTS:

If you don't already have ~tidyr~ and ~dplyr~ installed, you need to
do that before running the following:

#+BEGIN_SRC R :results output
library(tidyr)
library(dplyr)
as_tibble(iris)
#+END_SRC

#+RESULTS:
#+begin_example
# A tibble: 150 x 5
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
          <dbl>       <dbl>        <dbl>       <dbl> <fct>  
 1         5.10        3.50         1.40       0.200 setosa 
 2         4.90        3.00         1.40       0.200 setosa 
 3         4.70        3.20         1.30       0.200 setosa 
 4         4.60        3.10         1.50       0.200 setosa 
 5         5.00        3.60         1.40       0.200 setosa 
 6         5.40        3.90         1.70       0.400 setosa 
 7         4.60        3.40         1.40       0.300 setosa 
 8         5.00        3.40         1.50       0.200 setosa 
 9         4.40        2.90         1.40       0.200 setosa 
10         4.90        3.10         1.50       0.100 setosa 
# ... with 140 more rows
#+end_example

#+BEGIN_SRC R :results output :session RSESSION
library(tidyr)
library(dplyr)
as_tibble(iris)
#+END_SRC

#+RESULTS:
#+begin_example

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union
# A tibble: 150 x 5
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
          <dbl>       <dbl>        
<dbl>       <dbl> 
<fct>  
 1         5.10        3.50         1.40       
0.200 setosa 
 2         4.90        3.00         1.40       
0.200 setosa 
 3         4.70        3.20         1.30       
0.200 setosa 
 4         4.60        3.10         1.50       
0.200 setosa 
 5         5.00        3.60         1.40       
0.200 setosa 
 6         5.40        3.90         1.70       
0.400 setosa 
 7         4.60        3.40         1.40       
0.300 setosa 
 8         5.00        3.40         1.50       
0.200 setosa 
 9         4.40        2.90         1.40       
0.200 setosa 
10         4.90        3.10         1.50       
0.100 setosa 
# ... with 140 more rows
#+end_example

* Proposed Fix

Evaluating the following replaces the built-in function with my fix:

#+BEGIN_SRC elisp fix
(defun org-babel-R-evaluate-session
    (session body result-type result-params column-names-p row-names-p)
  "Evaluate BODY in SESSION.
If RESULT-TYPE equals `output' then return standard output as a
string.  If RESULT-TYPE equals `value' then return the value of the
last statement in BODY, as elisp."
  (cl-case result-type
    (value
     (with-temp-buffer
       (insert (org-babel-chomp body))
       (let ((ess-local-process-name
              (process-name (get-buffer-process session)))
             (ess-eval-visibly-p nil))
         (ess-eval-buffer nil)))
     (let ((tmp-file (org-babel-temp-file "R-")))
       (org-babel-comint-eval-invisibly-and-wait-for-file
        session tmp-file
        (format org-babel-R-write-object-command
                (if row-names-p "TRUE" "FALSE")
                (if column-names-p
                    (if row-names-p "NA" "TRUE")
                  "FALSE")
                ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
       (org-babel-R-process-value-result
        (org-babel-result-cond result-params
          (with-temp-buffer
            (insert-file-contents tmp-file)
            (org-babel-chomp (buffer-string) "\n"))
          (org-babel-import-elisp-from-file tmp-file '(16)))
        column-names-p)))
    (output
     ;; strip ansi-color-control-seq-regexp from output!!
     (replace-regexp-in-string
      ansi-color-control-seq-regexp ""
      (mapconcat
       'org-babel-chomp
       (butlast
        (delq nil
              (mapcar
               (lambda (line) (when (> (length line) 0) line))
               (mapcar
                (lambda (line) ;; cleanup extra prompts left in output
                  (if (string-match
                       "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
                       (car (split-string line "\n")))
                      (substring line (match-end 1))
                    line))
                (org-babel-comint-with-output (session org-babel-R-eoe-output)
                  (insert (mapconcat 'org-babel-chomp
                                     (list body org-babel-R-eoe-indicator)
                                     "\n"))
                  (inferior-ess-send-input)))))) "\n")))))

#+END_SRC

#+RESULTS:
: org-babel-R-evaluate-session

#+BEGIN_SRC R :results output :session RSESSION
as_tibble(iris)
#+END_SRC

#+RESULTS:
#+begin_example
# A tibble: 150 x 5
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
          <dbl>       <dbl>        <dbl>       <dbl> <fct>  
 1         5.10        3.50         1.40       0.200 setosa 
 2         4.90        3.00         1.40       0.200 setosa 
 3         4.70        3.20         1.30       0.200 setosa 
 4         4.60        3.10         1.50       0.200 setosa 
 5         5.00        3.60         1.40       0.200 setosa 
 6         5.40        3.90         1.70       0.400 setosa 
 7         4.60        3.40         1.40       0.300 setosa 
 8         5.00        3.40         1.50       0.200 setosa 
 9         4.40        2.90         1.40       0.200 setosa 
10         4.90        3.10         1.50       0.100 setosa 
# ... with 140 more rows
#+end_example