From 08cdd0557967d69a093b1642a4467e800fe84c4b Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Mon, 30 Aug 2010 09:26:02 -0700
Subject: [PATCH] babel: Cleaner session evaluation for R in :results value
 case

    * ob-comint.el (org-babel-comint-eval-invisibly-and-wait-for-file): New
    function to evaluate code invisibly and block until output file exists.
    * ob-R.el (org-babel-R-evaluate-session): Use
    `ess-eval-buffer' to evaluate R code in session for :results
    value. Write result to file invisibly using new function
    `org-babel-comint-eval-invisibly-and-wait-for-file'.

These changes move to using standard ESS code evaluation in R sessions
in the :results value case, which avoids unnecessary output to the
comint buffer. In addition, the R command responsible for writing the
result to file is hidden from the user.
---
 lisp/ob-R.el      | 17 ++++++++---------
 lisp/ob-comint.el | 17 +++++++++++++++++
 2 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index d16b659f3..e726d034a 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -259,21 +259,20 @@ string. If RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (case result-type
     (value
-     (let ((tmp-file (org-babel-temp-file "R-"))
-	   broke)
-       (org-babel-comint-with-output (session org-babel-R-eoe-output)
-	 (insert (mapconcat
-		  #'org-babel-chomp
-		  (list
-		   body
+     (with-temp-buffer
+       (insert (org-babel-chomp body))
+       (let ((ess-local-process-name
+	      (process-name (get-buffer-process session))))
+	 (ess-eval-buffer nil)))
+     (let ((tmp-file (org-babel-temp-file "R-")))
+       (org-babel-comint-eval-invisibly-and-wait-for-file
+	session (org-babel-maybe-remote-file tmp-file)
 		   (format org-babel-R-wrapper-lastvar
 			   tmp-file
 			   (if row-names-p "TRUE" "FALSE")
 			   (if column-names-p
 			       (if row-names-p "NA" "TRUE")
 			     "FALSE"))
-		   org-babel-R-eoe-indicator) "\n"))
-	 (inferior-ess-send-input))
        (org-babel-R-process-value-result
 	(org-babel-import-elisp-from-file
 	 (org-babel-maybe-remote-file tmp-file) '(16))  column-names-p)))
diff --git a/lisp/ob-comint.el b/lisp/ob-comint.el
index c7d3d14a0..ff7f0cba9 100644
--- a/lisp/ob-comint.el
+++ b/lisp/ob-comint.el
@@ -136,6 +136,23 @@ statement (not large blocks of code)."
                                 "comint-highlight-prompt"))))
       (accept-process-output (get-buffer-process buffer)))))
 
+(defun org-babel-comint-eval-invisibly-and-wait-for-file
+  (buffer file string &optional period)
+  "Evaluate STRING in BUFFER invisibly.
+Don't return until FILE exists. Code in STRING must ensure that
+FILE exists at end of evaluation."
+  (unless (org-babel-comint-buffer-livep buffer)
+    (error "buffer %s doesn't exist or has no process" buffer))
+  (if (file-exists-p file) (delete-file file))
+  (process-send-string
+   (get-buffer-process buffer)
+   (if (string-match "\n$" string) string (concat string "\n")))
+  ;; From Tramp 2.1.19 the following cache flush is not necessary
+  (if (file-remote-p default-directory)
+      (with-parsed-tramp-file-name default-directory nil
+	(tramp-flush-directory-property v "")))
+  (while (not (file-exists-p file)) (sit-for (or period 0.25))))
+
 (provide 'ob-comint)
 
 ;; arch-tag: 9adddce6-0864-4be3-b0b5-6c5157dc7889