Re-apply commit 27bcf9a together with a workaround for `process-file'.

Thanks to Michael Albinus for hunting this bug and for providing
this workaround.

lisp/ob-eval.el

@@ -135,15 +135,19 @@ specifies the value of ERROR-BUFFER."
 		       current-prefix-arg
 		       shell-command-default-error-buffer
 		       t)))
-  (let ((error-file
-	 (if error-buffer
-	     (make-temp-file
-	      (expand-file-name "scor"
-                                (if (featurep 'xemacs)
-                                    (temp-directory)
-                                  temporary-file-directory)))
-	   nil))
+  (let ((input-file (org-babel-temp-file "input-"))
+	(error-file (if error-buffer (org-babel-temp-file "scor-") nil))
+	(shell-file-name
+	 (if (file-executable-p
+	      (concat (file-remote-p default-directory) shell-file-name))
+	     shell-file-name
+	   "/bin/sh"))
 	exit-status)
+    ;; There is an error in `process-file' when `error-file' exists.
+    ;; This is fixed in Emacs trunk as of 2012-12-21; let's use this
+    ;; workaround for now.
+    (unless (file-remote-p default-directory)
+      (delete-file error-file))
     (if (or replace
 	    (and output-buffer
 		 (not (or (bufferp output-buffer) (stringp output-buffer)))))
@@ -152,12 +156,14 @@ specifies the value of ERROR-BUFFER."
 	  ;; Don't muck with mark unless REPLACE says we should.
 	  (goto-char start)
 	  (and replace (push-mark (point) 'nomsg))
+	  (write-region start end input-file)
+	  (delete-region start end)
 	  (setq exit-status
-		(call-process-region start end shell-file-name t
-				     (if error-file
-					 (list output-buffer error-file)
-				       t)
-				     nil shell-command-switch command))
+		(process-file shell-file-name input-file
+			      (if error-file
+				  (list output-buffer error-file)
+				t)
+			      nil shell-command-switch command))
 	  ;; It is rude to delete a buffer which the command is not using.
 	  ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
 	  ;;   (and shell-buffer (not (eq shell-buffer (current-buffer)))
@@ -176,14 +182,14 @@ specifies the value of ERROR-BUFFER."
 		(progn (setq buffer-read-only nil)
 		       (delete-region (max start end) (point-max))
 		       (delete-region (point-min) (min start end))
+		       (write-region (point-min) (point-max) input-file)
+		       (delete-region (point-min) (point-max))
 		       (setq exit-status
-			     (call-process-region (point-min) (point-max)
-						  shell-file-name t
-						  (if error-file
-						      (list t error-file)
-						    t)
-						  nil shell-command-switch
-						  command)))
+			     (process-file shell-file-name input-file
+					   (if error-file
+					       (list t error-file)
+					     t)
+					   nil shell-command-switch command)))
 	      ;; Clear the output buffer, then run the command with
 	      ;; output there.
 	      (let ((directory default-directory))
@@ -193,11 +199,11 @@ specifies the value of ERROR-BUFFER."
 		      (setq default-directory directory))
 		  (erase-buffer)))
 	      (setq exit-status
-		    (call-process-region start end shell-file-name nil
-					 (if error-file
-					     (list buffer error-file)
-					   buffer)
-					 nil shell-command-switch command)))
+		    (process-file shell-file-name nil
+				  (if error-file
+				      (list buffer error-file)
+				    buffer)
+				  nil shell-command-switch command)))
 	  ;; Report the output.
 	  (with-current-buffer buffer
 	    (setq mode-line-process
@@ -231,6 +237,9 @@ specifies the value of ERROR-BUFFER."
 	    ;; (kill-buffer buffer)
 	    ))))
 
+    (when (and input-file (file-exists-p input-file))
+      (delete-file input-file))
+
     (when (and error-file (file-exists-p error-file))
       (if (< 0 (nth 7 (file-attributes error-file)))
 	  (with-current-buffer (get-buffer-create error-buffer)

lisp/ob.el

@@ -2547,18 +2547,14 @@ Emacs shutdown."))
 Passes PREFIX and SUFFIX directly to `make-temp-file' with the
 value of `temporary-file-directory' temporarily set to the value
 of `org-babel-temporary-directory'."
-  (if (file-remote-p default-directory)
-      (make-temp-file
-       (concat (file-remote-p default-directory)
-	       (expand-file-name
-		prefix temporary-file-directory)
-	       nil suffix))
-    (let ((temporary-file-directory
+  (let ((temporary-file-directory
+	 (if (file-remote-p default-directory)
+	     (concat (file-remote-p default-directory) "/tmp")
 	   (or (and (boundp 'org-babel-temporary-directory)
 		    (file-exists-p org-babel-temporary-directory)
 		    org-babel-temporary-directory)
-	       temporary-file-directory)))
-      (make-temp-file prefix nil suffix))))
+	       temporary-file-directory))))
+      (make-temp-file prefix nil suffix)))
 
 (defun org-babel-remove-temporary-directory ()
   "Remove `org-babel-temporary-directory' on Emacs shutdown."