fixed non-session variable assignment in R

lisp/langs/org-babel-R.el

@@ -39,21 +39,24 @@ called by `org-babel-execute-src-block'."
   (message "executing R source code block...")
   (save-window-excursion
     (let* ((vars (org-babel-ref-variables params))
+           (full-body (concat
+                       (mapconcat ;; define any variables
+                        (lambda (pair)
+                          (org-babel-R-assign-elisp (car pair) (cdr pair)))
+                        vars "\n") "\n" body "\n"))
            (result-params (split-string (or (cdr (assoc :results params)) "")))
            (result-type (cond ((member "output" result-params) 'output)
                               ((member "value" result-params) 'value)
                               (t 'value)))
            (session (org-babel-R-initiate-session (cdr (assoc :session params))))
            results)
-      ;; assign variables
-      (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)
       ;; ;;; debugging statements
       ;; (message (format "result-type=%S" result-type))
       ;; (message (format "body=%S" body))
       ;; (message (format "session=%S" session))
       ;; (message (format "result-params=%S" result-params))
       ;; evaluate body and convert the results to ruby
-      (setq results (org-babel-R-evaluate session body result-type))
+      (setq results (org-babel-R-evaluate session full-body result-type))
       (setq results (if (member "scalar" result-params)
                         results
                       (let ((tmp-file (make-temp-file "org-babel-R")))
@@ -77,22 +80,18 @@ called by `org-babel-execute-src-block'."
       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
     (format "%S" s)))
 
-(defun org-babel-R-assign-elisp (session name value)
-  "Read the elisp VALUE into a variable named NAME in the current
-R process in `org-babel-R-buffer'."
-  (unless session (error "No active R buffer"))
-  (org-babel-comint-input-command
-   session
-   (if (listp value)
-       (let ((transition-file (make-temp-file "org-babel-R-import")))
-	 ;; ensure VALUE has an orgtbl structure (depth of at least 2)
-	 (unless (listp (car value)) (setq value (list value)))
-	 (with-temp-file transition-file
-	   (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
-	   (insert "\n"))
-	 (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
-		 name transition-file))
-     (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))))
+(defun org-babel-R-assign-elisp (name value)
+  "Read the elisp VALUE into a variable named NAME."
+  (if (listp value)
+      (let ((transition-file (make-temp-file "org-babel-R-import")))
+        ;; ensure VALUE has an orgtbl structure (depth of at least 2)
+        (unless (listp (car value)) (setq value (list value)))
+        (with-temp-file transition-file
+          (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
+          (insert "\n"))
+        (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
+                name transition-file))
+    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 
 (defun org-babel-R-initiate-session (session)
   "If there is not a current R process then create one."

org-babel.org

@@ -2218,52 +2218,52 @@ org-babel functionality.
 of these tests may fail.
 
 #+TBLNAME: org-babel-tests
-| functionality           | block                      | arg |    expected |     results | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| basic evaluation        |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| emacs lisp              | basic-elisp                |     |           5 |           5 | pass                            |
-| shell                   | basic-shell                |     |           6 |           6 | pass                            |
-| ruby                    | basic-ruby                 |     |   org-babel |   org-babel | pass                            |
-| python                  | basic-python               |     | hello world | hello world | pass                            |
-| R                       | basic-R                    |     |          13 |          13 | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| tables                  |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| emacs lisp              | table-elisp                |     |           3 |           3 | pass                            |
-| ruby                    | table-ruby                 |     |       1-2-3 |       1-2-3 | pass                            |
-| python                  | table-python               |     |           5 |           5 | pass                            |
-| R                       | table-R                    |     |         3.5 |      #ERROR | expected "3.5" but was "#ERROR" |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| source block references |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| all languages           | chained-ref-last           |     |       Array |       Array | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| source block functions  |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| emacs lisp              | defun-fibb                 |     |       fibbd |       fibbd | pass                            |
-| run over                | Fibonacci                  |   0 |           1 |           1 | pass                            |
-| a                       | Fibonacci                  |   1 |           1 |           1 | pass                            |
-| variety                 | Fibonacci                  |   2 |           2 |           2 | pass                            |
-| of                      | Fibonacci                  |   3 |           3 |           3 | pass                            |
-| different               | Fibonacci                  |   4 |           5 |           5 | pass                            |
-| arguments               | Fibonacci                  |   5 |           8 |           8 | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| bugs and tasks          |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| simple ruby arrays      | ruby-array-test            |     |           3 |           3 | pass                            |
-| R number evaluation     | bug-R-number-evaluation    |     |           2 |      #ERROR | expected "2" but was "#ERROR"   |
-| multi-line ruby blocks  | multi-line-ruby-test       |     |           2 |           2 | pass                            |
-| forcing vector results  | test-forced-vector-results |     |       Array |       Array | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| sessions                |                            |     |             |             | pass                            |
-|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------|
-| set ruby session        | set-ruby-session-var       |     |        :set |        :set | pass                            |
-| get from ruby session   | get-ruby-session-var       |     |           3 |             | expected "3" but was ""         |
-| set python session      | set-python-session-var     |     |         set |         set | pass                            |
-| get from python session | get-python-session-var     |     |           4 |             | expected "4" but was ""         |
-| set R session           | set-R-session-var          |     |         set |         set | pass                            |
-| get from R session      | get-R-session-var          |     |           5 |         nil | expected "5" but was "nil"      |
+| functionality           | block                      | arg |    expected |     results | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| basic evaluation        |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| emacs lisp              | basic-elisp                |     |           5 |           5 | pass                       |
+| shell                   | basic-shell                |     |           6 |           6 | pass                       |
+| ruby                    | basic-ruby                 |     |   org-babel |   org-babel | pass                       |
+| python                  | basic-python               |     | hello world | hello world | pass                       |
+| R                       | basic-R                    |     |          13 |          13 | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| tables                  |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| emacs lisp              | table-elisp                |     |           3 |           3 | pass                       |
+| ruby                    | table-ruby                 |     |       1-2-3 |       1-2-3 | pass                       |
+| python                  | table-python               |     |           5 |           5 | pass                       |
+| R                       | table-R                    |     |         3.5 |         3.5 | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| source block references |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| all languages           | chained-ref-last           |     |       Array |       Array | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| source block functions  |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| emacs lisp              | defun-fibb                 |     |       fibbd |       fibbd | pass                       |
+| run over                | Fibonacci                  |   0 |           1 |           1 | pass                       |
+| a                       | Fibonacci                  |   1 |           1 |           1 | pass                       |
+| variety                 | Fibonacci                  |   2 |           2 |           2 | pass                       |
+| of                      | Fibonacci                  |   3 |           3 |           3 | pass                       |
+| different               | Fibonacci                  |   4 |           5 |           5 | pass                       |
+| arguments               | Fibonacci                  |   5 |           8 |           8 | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| bugs and tasks          |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| simple ruby arrays      | ruby-array-test            |     |           3 |           3 | pass                       |
+| R number evaluation     | bug-R-number-evaluation    |     |           2 |           2 | pass                       |
+| multi-line ruby blocks  | multi-line-ruby-test       |     |           2 |           2 | pass                       |
+| forcing vector results  | test-forced-vector-results |     |       Array |       Array | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| sessions                |                            |     |             |             | pass                       |
+|-------------------------+----------------------------+-----+-------------+-------------+----------------------------|
+| set ruby session        | set-ruby-session-var       |     |        :set |        :set | pass                       |
+| get from ruby session   | get-ruby-session-var       |     |           3 |             | expected "3" but was ""    |
+| set python session      | set-python-session-var     |     |         set |         set | pass                       |
+| get from python session | get-python-session-var     |     |           4 |             | expected "4" but was ""    |
+| set R session           | set-R-session-var          |     |         set |         set | pass                       |
+| get from R session      | get-R-session-var          |     |           5 |         nil | expected "5" but was "nil" |
 #+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
 
 ** basic tests