Re: Help debugging R source code block output problem with :session

[Jack Kamm <jackkamm@gmail.com>]

[-- Attachment #1: Type: text/plain, Size: 744 bytes --]

Hi Dylan,

I'm able to reproduce your error. I think this same bug has been
previously reported at [1]. As discussed there, the reason is that
substrings ending in ">" get stripped out by
org-babel-comint-with-output because it thinks they are prompts (in
particular, they match comint-prompt-regexp).

I'm attaching a patch to solve the issue. It replaces
org-babel-comint-with-output, with an R call to capture.output. I think
this approach is simpler and more robust, since it doesn't need to do
any parsing to remove prompts or other unwanted outputs.

I haven't committed to ob-R.el before, so thought it would be best to
solicit feedback here before merging this in.

Cheers,
Jack

[1] https://orgmode.org/list/875zgjh8wn.fsf@gmail.com/


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-ob-R-Fix-prompt-mangling-in-session-output.patch --]
[-- Type: text/x-patch, Size: 3698 bytes --]

From 1dc8e2d2cb01a4e6b82342ea8d8c965df8f5222c Mon Sep 17 00:00:00 2001
From: Jack Kamm <jackkamm@gmail.com>
Date: Fri, 28 Aug 2020 19:16:05 -0700
Subject: [PATCH] ob-R: Fix prompt mangling in session output

* lisp/ob-R.el (org-babel-R-evaluate-session): Replace
call to org-babel-comint-with-output with ess-send-to-buffer and
additional wrapper R code.

Fixes https://orgmode.org/list/875zgjh8wn.fsf@gmail.com/ and
https://orgmode.org/list/87r1rqled0.fsf@havana/
---
 lisp/ob-R.el | 79 ++++++++++++++++++++++++----------------------------
 1 file changed, 36 insertions(+), 43 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 5e9d35f58..d69cf23db 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -412,49 +412,42 @@ (defun org-babel-R-evaluate-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
-     (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"))))
+  (let ((ess-local-process-name
+	 (process-name (get-buffer-process session)))
+	(ess-eval-visibly-p nil))
+    (cl-case result-type
+      (value
+       (with-temp-buffer
+	 (insert (org-babel-chomp body))
+	 (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
+       (let ((tmp-file (org-babel-temp-file "R-")))
+	 (with-temp-buffer
+	   (insert (format "capture.output({
+%s
+}, file='%s')"
+			   body tmp-file))
+	   (ess-eval-buffer))
+	 (ess-wait-for-process)
+	 (with-temp-buffer
+	   (insert-file-contents tmp-file)
+	   (buffer-string)))))))
 
 (defun org-babel-R-process-value-result (result column-names-p)
   "R-specific processing of return value.
-- 
2.28.0