babel: Provide notification of errors during code execution

This deals with external process :results value mode for R, ruby,
python, perl and clojure: if the shell process has a non-zero exit
code, a buffer containing stderr is displayed.

contrib/babel/lisp/langs/org-babel-R.el

@@ -142,18 +142,22 @@ BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (if (not session)
       ;; external process evaluation
-      (let ((tmp-file (make-temp-file "R-out-functional-results")))
-        (case result-type
-          (output
-	   (with-temp-buffer
-             (insert body)
-             (org-babel-shell-command-on-region (point-min) (point-max) "R --slave --no-save" 'current-buffer 'replace)
-             (buffer-string)))
-          (value
-	   (with-temp-buffer
-             (insert (format org-babel-R-wrapper-method
-			     body tmp-file (if column-names-p "TRUE" "FALSE")))
-	     (org-babel-shell-command-on-region (point-min) (point-max) "R --no-save"))
+      (case result-type
+	(output
+	 (with-temp-buffer
+	   (insert body)
+	   (org-babel-shell-command-on-region (point-min) (point-max) "R --slave --no-save" 'current-buffer 'replace)
+	   (buffer-string)))
+	(value
+	 (let* ((tmp-file (make-temp-file "R-out-functional-results")) exit-code
+		(stderr
+		 (with-temp-buffer
+		   (insert (format org-babel-R-wrapper-method
+				   body tmp-file (if column-names-p "TRUE" "FALSE")))
+		   (setq exit-code (org-babel-shell-command-on-region
+				    (point-min) (point-max) "R --no-save" nil 'replace (current-buffer)))
+		   (buffer-string))))
+	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
 	   (org-babel-R-process-value-result
 	    (org-babel-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))
 	    column-names-p))))

contrib/babel/lisp/langs/org-babel-clojure.el

@@ -219,25 +219,27 @@ or nil if \"none\" is specified"
 
 (defun org-babel-clojure-evaluate-external-process (buffer body &optional result-type)
   "Evaluate the body in an external process."
-  (save-window-excursion
-    (case result-type
-      (output
-       (with-temp-buffer
-         (insert body)
-         (org-babel-shell-command-on-region
-          (point-min) (point-max)
-          (format "%s - " (mapconcat #'identity (org-babel-clojure-babel-clojure-cmd) " "))
-          'current-buffer 'replace)
-         (buffer-string)))
-      (value
-       (let ((tmp-results-file (make-temp-file "clojure_babel_results_")))
-         (with-temp-buffer
-           (insert (format org-babel-clojure-wrapper-method body tmp-results-file tmp-results-file))
-	   (org-babel-shell-command-on-region
-	    (point-min) (point-max)
-	    (format "%s - " (mapconcat #'identity (org-babel-clojure-babel-clojure-cmd) " "))))
-         (org-babel-clojure-table-or-string
-          (with-temp-buffer (insert-file-contents (org-babel-maybe-remote-file tmp-results-file)) (buffer-string))))))))
+  (save-excursion
+    (let ((cmd (format "%s -" (mapconcat #'identity (org-babel-clojure-babel-clojure-cmd) " "))))
+      (case result-type
+	(output
+	 (with-temp-buffer
+	   (insert body)
+	   (org-babel-shell-command-on-region cmd (point-min) (point-max) 'current-buffer 'replace)
+	   (buffer-string)))
+	(value
+	 (let* ((tmp-file (make-temp-file "org-babel-clojure-results-")) exit-code
+		(stderr
+		 (with-temp-buffer
+		   (insert
+		    (format org-babel-clojure-wrapper-method body tmp-file tmp-file))
+		   (setq exit-code
+			 (org-babel-shell-command-on-region (point-min) (point-max) cmd nil 'replace (current-buffer)))
+		   (buffer-string))))
+	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
+	   (org-babel-clojure-table-or-string
+	    (with-temp-buffer
+	      (insert-file-contents (org-babel-maybe-remote-file tmp-file)) (buffer-string)))))))))
 
 (defun org-babel-clojure-evaluate-session (buffer body &optional result-type)
   "Evaluate the body in the context of a clojure session"

contrib/babel/lisp/langs/org-babel-perl.el

@@ -92,7 +92,7 @@ BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (if (not session)
       ;; external process evaluation
-      (save-window-excursion
+      (save-excursion
         (case result-type
           (output
            (with-temp-buffer
@@ -101,20 +101,25 @@ last statement in BODY, as elisp."
              (org-babel-shell-command-on-region (point-min) (point-max) "perl" 'current-buffer 'replace)
              (buffer-string)))
           (value
-           (let ((tmp-file (make-temp-file "perl-functional-results")))
-             (with-temp-buffer
-               (insert
-		(format
-		 (if (member "pp" result-params)
-                     (error "Pretty-printing not implemented for perl")
-                   org-babel-perl-wrapper-method)
-		 (mapconcat
-		  (lambda (line) (format "\t%s" line))
-		  (split-string
-		   (org-remove-indentation (org-babel-trim body)) "[\r\n]") "\n")
-		 tmp-file))
-               ;; (message "buffer=%s" (buffer-string)) ;; debugging
-               (org-babel-shell-command-on-region (point-min) (point-max) "perl"))
+           (let* ((tmp-file (make-temp-file "perl-functional-results")) exit-code
+		 (stderr
+		  (with-temp-buffer
+		    (insert
+		     (format
+		      (if (member "pp" result-params)
+			  (error "Pretty-printing not implemented for perl")
+			org-babel-perl-wrapper-method)
+		      (mapconcat
+		       (lambda (line) (format "\t%s" line))
+		       (split-string
+			(org-remove-indentation (org-babel-trim body)) "[\r\n]") "\n")
+		      tmp-file))
+		    ;; (message "buffer=%s" (buffer-string)) ;; debugging
+		    (setq exit-code
+			  (org-babel-shell-command-on-region
+			   (point-min) (point-max) "perl" nil 'replace (current-buffer)))
+		    (buffer-string))))
+	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
 	     (org-babel-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))))))
     ;; comint session evaluation
     (error "Sessions are not supported for Perl.")))

contrib/babel/lisp/langs/org-babel-python.el

@@ -155,7 +155,7 @@ BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (if (not session)
       ;; external process evaluation
-      (save-window-excursion
+      (save-excursion
         (case result-type
           (output
            (with-temp-buffer
@@ -164,20 +164,24 @@ last statement in BODY, as elisp."
              (org-babel-shell-command-on-region (point-min) (point-max) "python" 'current-buffer 'replace)
              (buffer-string)))
           (value
-           (let ((tmp-file (make-temp-file "python-functional-results")))
-             (with-temp-buffer
-               (insert
-		(format
-		 (if (member "pp" result-params)
-                     org-babel-python-pp-wrapper-method
-                   org-babel-python-wrapper-method)
-		 (mapconcat
-		  (lambda (line) (format "\t%s" line))
-		  (split-string
-		   (org-remove-indentation (org-babel-trim body)) "[\r\n]") "\n")
-		 tmp-file))
-               ;; (message "buffer=%s" (buffer-string)) ;; debugging
-               (org-babel-shell-command-on-region (point-min) (point-max) "python"))
+           (let* ((tmp-file (make-temp-file "org-babel-python-results-")) exit-code
+		  (stderr
+		   (with-temp-buffer
+		     (insert
+		      (format
+		       (if (member "pp" result-params)
+			   org-babel-python-pp-wrapper-method
+			 org-babel-python-wrapper-method)
+		       (mapconcat
+			(lambda (line) (format "\t%s" line))
+			(split-string
+			 (org-remove-indentation (org-babel-trim body)) "[\r\n]") "\n")
+		       tmp-file))
+		     ;; (message "buffer=%s" (buffer-string)) ;; debugging
+		     (setq exit-code (org-babel-shell-command-on-region
+				      (point-min) (point-max) "python" nil 'replace (current-buffer)))
+		     (buffer-string))))
+	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
              (let ((raw (with-temp-buffer
 			  (insert-file-contents (org-babel-maybe-remote-file tmp-file))
 			  (buffer-string))))

contrib/babel/lisp/langs/org-babel-ruby.el

@@ -159,7 +159,7 @@ BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (if (not session)
       ;; external process evaluation
-      (save-window-excursion
+      (save-excursion
         (case result-type
           (output
            (with-temp-buffer
@@ -168,13 +168,17 @@ last statement in BODY, as elisp."
              (org-babel-shell-command-on-region (point-min) (point-max) "ruby" 'current-buffer 'replace)
              (buffer-string)))
           (value
-           (let ((tmp-file (make-temp-file "ruby-functional-results")))
-             (with-temp-buffer
-               (insert (format (if (member "pp" result-params)
-                                   org-babel-ruby-pp-wrapper-method
-                                 org-babel-ruby-wrapper-method) body tmp-file))
-               ;; (message "buffer=%s" (buffer-string)) ;; debugging
-               (org-babel-shell-command-on-region (point-min) (point-max) "ruby"))
+           (let* ((tmp-file (make-temp-file "ruby-functional-results")) exit-code
+		  (stderr
+		   (with-temp-buffer
+		     (insert (format (if (member "pp" result-params)
+					 org-babel-ruby-pp-wrapper-method
+				       org-babel-ruby-wrapper-method) body tmp-file))
+		     ;; (message "buffer=%s" (buffer-string)) ;; debugging
+		     (setq exit-code
+			   (org-babel-shell-command-on-region (point-min) (point-max) "ruby" nil 'replace (current-buffer)))
+		     (buffer-string))))
+	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
              (let ((raw (with-temp-buffer
 			  (insert-file-contents (org-babel-maybe-remote-file tmp-file))
 			  (buffer-string))))

contrib/babel/lisp/org-babel.el

@@ -1022,6 +1022,14 @@ block but are passed literally to the \"example-block\"."
         (nb-add (buffer-substring index (point-max)))))
     new-body))
 
+(defun org-babel-error-notify (exit-code stderr)
+  (message (format "Shell command exited with code %d" exit-code))
+  (let ((buf (get-buffer-create "*Org-Babel Error Output*")))
+    (with-current-buffer buf
+      (goto-char (point-max))
+      (save-excursion (insert stderr)))
+    (display-buffer buf)))
+
 (defun org-babel-clean-text-properties (text)
   "Strip all properties from text return."
   (set-text-properties 0 (length text) nil text) text)
@@ -1055,22 +1063,23 @@ This is taken almost directly from `org-read-prop'."
   "Read the results located at FILE-NAME into an elisp table.  If
 the table is trivial, then return it as a scalar."
   (let (result)
-    (with-temp-buffer
-      (condition-case nil
-          (progn
-            (org-table-import file-name nil)
-            (delete-file file-name)
-            (setq result (mapcar (lambda (row)
-                                   (mapcar #'org-babel-string-read row))
-                                 (org-table-to-lisp))))
-        (error nil)))
-    (if (null (cdr result)) ;; if result is trivial vector, then scalarize it
-	(if (consp (car result))
-	    (if (null (cdr (car result)))
-		(caar result)
-	      result)
-	  (car result))
-      result)))
+    (save-window-excursion
+      (with-temp-buffer
+	(condition-case nil
+	    (progn
+	      (org-table-import file-name nil)
+	      (delete-file file-name)
+	      (setq result (mapcar (lambda (row)
+				     (mapcar #'org-babel-string-read row))
+				   (org-table-to-lisp))))
+	  (error nil)))
+      (if (null (cdr result)) ;; if result is trivial vector, then scalarize it
+	  (if (consp (car result))
+	      (if (null (cdr (car result)))
+		  (caar result)
+		result)
+	    (car result))
+	result))))
 
 (defun org-babel-string-read (cell)
   "Strip nested \"s from around strings in exported R values."