Hi,
The printed output of some R functions includes ascii color codes (i.e.,
[3m[90m). 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
[90m# A tibble: 150 x 5[39m
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
[3m[90m<dbl>[39m[23m [3m[90m<dbl>[39m[23m
[3m[90m<dbl>[39m[23m [3m[90m<dbl>[39m[23m
[3m[90m<fct>[39m[23m
[90m 1[39m 5.10 3.50 1.40
[90m0[39m[90m.[39m200 setosa
[90m 2[39m 4.90 3.00 1.40
[90m0[39m[90m.[39m200 setosa
[90m 3[39m 4.70 3.20 1.30
[90m0[39m[90m.[39m200 setosa
[90m 4[39m 4.60 3.10 1.50
[90m0[39m[90m.[39m200 setosa
[90m 5[39m 5.00 3.60 1.40
[90m0[39m[90m.[39m200 setosa
[90m 6[39m 5.40 3.90 1.70
[90m0[39m[90m.[39m400 setosa
[90m 7[39m 4.60 3.40 1.40
[90m0[39m[90m.[39m300 setosa
[90m 8[39m 5.00 3.40 1.50
[90m0[39m[90m.[39m200 setosa
[90m 9[39m 4.40 2.90 1.40
[90m0[39m[90m.[39m200 setosa
[90m10[39m 4.90 3.10 1.50
[90m0[39m[90m.[39m100 setosa
[90m# ... with 140 more rows[39m
#+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
