From afa24835f2a170c59a044dcf3bcf0ee765e8b568 Mon Sep 17 00:00:00 2001
From: Aaron Ecay <aaronecay@gmail.com>
Date: Sat, 16 Aug 2014 00:49:05 -0400
Subject: [PATCH] ob-R: overhaul handling of :output results type in a session
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* (org-babel-R-evaluate-session): Capture output using ‘ess-execute’.

This function dumps the output from R into a buffer; we then use some
tricks to clean it of spurious text.
---
 lisp/ob-R.el | 69 ++++++++++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 51 insertions(+), 18 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 41b943c..fbd4af4 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -364,9 +364,10 @@ last statement in BODY, as elisp."
     (output (org-babel-eval org-babel-R-command body))))
 
 (defvar ess-eval-visibly-p)
+(defvar ess-execute-in-process-buffer)
 
 (defun org-babel-R-evaluate-session
-  (session body result-type result-params column-names-p row-names-p)
+    (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
@@ -396,23 +397,55 @@ last statement in BODY, as elisp."
 	  (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
-		      "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
-		     (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* ((sentinel-file (org-babel-temp-file "R-")))
+       ;; This code borrowed from
+       ;; `org-babel-comint-eval-invisibly-and-wait-for-file'
+       (unless (org-babel-comint-buffer-livep session)
+	 (error "Buffer %s does not exist or has no process" session))
+       (if (file-exists-p sentinel-file) (delete-file sentinel-file))
+       (with-current-buffer session
+	 (let ((ess-execute-in-process-buffer nil)
+	       (temp-buffer-show-function #'ignore))
+	   (ess-execute (format
+			 "
+.org.old.opts <- options(prompt = \"# Org babel prompt\\n\", continue = \"# Org babel prompt\\n\")
+cat(\"# Org babel begin output\n\")
+{
+%s
+#ORG-BABEL-OOPS\"#'
+}
+cat(\"# Org babel end output\n\")
+options(.org.old.opts)
+rm(.org.old.opts)
+file.create(%S)
+"
+			 (org-babel-chomp body)
+			 (if (tramp-tramp-file-p sentinel-file)
+			     (tramp-file-name-localname
+			      (tramp-dissect-file-name sentinel-file))
+			   sentinel-file))
+			nil "org-babel-R-output"))
+	 ;; From Tramp 2.1.19 the following cache flush is not necessary
+	 (if (file-remote-p default-directory)
+	     (let (v)
+	       (with-parsed-tramp-file-name default-directory nil
+		 (tramp-flush-directory-property v "")))))
+       (while (not (file-exists-p sentinel-file)) (sit-for 0.25))
+       ;; End borrowed code.
+       (with-current-buffer "*org-babel-R-output*"
+	 (goto-char (point-min))
+	 (when (search-forward "ORG-BABEL-OOPS")
+	   (user-error "Mismatched quotation marks in babel code; could not parse output."))
+	 (search-forward "# Org babel begin output")
+	 (delete-region (point-min) (1+ (point)))
+	 (goto-char (point-max))
+	 (search-backward "# Org babel end output")
+	 (delete-region (point) (point-max))
+	 (goto-char (point-min))
+	 (flush-lines "^$")
+	 (flush-lines "^# Org babel prompt$")
+	 (delete-trailing-whitespace)
+	 (buffer-string))))))
 
 (defun org-babel-R-process-value-result (result column-names-p)
   "R-specific processing of return value.
-- 
2.0.4