Merge from trunk

1 files changed, 122 insertions, 99 deletions

diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el
index d990d69b357..81d628e4206 100644
--- a/lisp/org/ob-R.el
+++ b/lisp/org/ob-R.el
@@ -2,10 +2,11 @@
 
 ;; Copyright (C) 2009, 2010  Free Software Foundation, Inc.
 
-;; Author: Eric Schulte, Dan Davison
+;; Author: Eric Schulte
+;;      Dan Davison
 ;; Keywords: literate programming, reproducible research, R, statistics
 ;; Homepage: http://orgmode.org
-;; Version: 7.01
+;; Version: 7.3
 
 ;; This file is part of GNU Emacs.
 
@@ -36,6 +37,9 @@
 (declare-function orgtbl-to-tsv "org-table" (table params))
 (declare-function R "ext:essd-r" (&optional start-args))
 (declare-function inferior-ess-send-input "ext:ess-inf" ())
+(declare-function ess-make-buffer-current "ext:ess-inf" ())
+(declare-function ess-eval-buffer "ext:ess-inf" (vis))
+(declare-function org-number-sequence "org-compat" (from &optional to inc))
 
 (defconst org-babel-header-arg-names:R
   '(width height bg units pointsize antialias quality compression
@@ -48,21 +52,11 @@
 (defvar org-babel-R-command "R --slave --no-save"
   "Name of command to use for executing R code.")
 
-(defun org-babel-expand-body:R (body params &optional processed-params)
+(defun org-babel-expand-body:R (body params)
   "Expand BODY according to PARAMS, return the expanded body."
-  (let* ((processed-params (or processed-params
-                               (org-babel-process-params params)))
-         (vars (mapcar
-                (lambda (i)
-                  (cons (car (nth i (nth 1 processed-params)))
-                        (org-babel-reassemble-table
-                         (cdr (nth i (nth 1 processed-params)))
-                         (cdr (nth i (nth 4 processed-params)))
-                         (cdr (nth i (nth 5 processed-params))))))
-                (number-sequence 0 (1- (length (nth 1 processed-params))))))
-         (out-file (cdr (assoc :file params))))
-    (mapconcat ;; define any variables
-     #'org-babel-trim
+  (let ((out-file (cdr (assoc :file params))))
+    (mapconcat
+     #'identity
      ((lambda (inside)
         (if out-file
             (append
@@ -70,49 +64,36 @@
              inside
              (list "dev.off()"))
           inside))
-      (append
-       (mapcar
-        (lambda (pair)
-          (org-babel-R-assign-elisp
-           (car pair) (cdr pair)
-           (equal "yes" (cdr (assoc :colnames params)))
-           (equal "yes" (cdr (assoc :rownames params)))))
-        vars)
-       (list body))) "\n")))
+      (append (org-babel-variable-assignments:R params)
+              (list body))) "\n")))
 
 (defun org-babel-execute:R (body params)
   "Execute a block of R code.
 This function is called by `org-babel-execute-src-block'."
   (save-excursion
-    (let* ((processed-params (org-babel-process-params params))
-           (result-type (nth 3 processed-params))
+    (let* ((result-type (cdr (assoc :result-type params)))
            (session (org-babel-R-initiate-session
-                     (first processed-params) params))
+                     (cdr (assoc :session params)) params))
            (colnames-p (cdr (assoc :colnames params)))
            (rownames-p (cdr (assoc :rownames params)))
            (out-file (cdr (assoc :file params)))
-           (full-body (org-babel-expand-body:R body params processed-params))
+           (full-body (org-babel-expand-body:R body params))
            (result
             (org-babel-R-evaluate
              session full-body result-type
              (or (equal "yes" colnames-p)
-                 (org-babel-pick-name (nth 4 processed-params) colnames-p))
+                 (org-babel-pick-name
+                  (cdr (assoc :colname-names params)) colnames-p))
              (or (equal "yes" rownames-p)
-                 (org-babel-pick-name (nth 5 processed-params) rownames-p)))))
+                 (org-babel-pick-name
+                  (cdr (assoc :rowname-names params)) rownames-p)))))
       (message "result is %S" result)
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
   (let* ((session (org-babel-R-initiate-session session params))
-         (vars (org-babel-ref-variables params))
-         (var-lines
-          (mapcar
-           (lambda (pair) (org-babel-R-assign-elisp
-                      (car pair) (cdr pair)
-                      (equal (cdr (assoc :colnames params)) "yes")
-                      (equal (cdr (assoc :rownames params)) "yes")))
-           vars)))
+         (var-lines (org-babel-variable-assignments:R params)))
     (org-babel-comint-in-buffer session
       (mapc (lambda (var)
               (end-of-line 1) (insert var) (comint-send-input nil t)
@@ -130,6 +111,24 @@ This function is called by `org-babel-execute-src-block'."
 
 ;; helper functions
 
+(defun org-babel-variable-assignments:R (params)
+  "Return list of R statements assigning the block's variables"
+  (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
+    (mapcar
+     (lambda (pair)
+       (org-babel-R-assign-elisp
+        (car pair) (cdr pair)
+        (equal "yes" (cdr (assoc :colnames params)))
+        (equal "yes" (cdr (assoc :rownames params)))))
+     (mapcar
+      (lambda (i)
+        (cons (car (nth i vars))
+              (org-babel-reassemble-table
+               (cdr (nth i vars))
+               (cdr (nth i (cdr (assoc :colname-names params))))
+               (cdr (nth i (cdr (assoc :rowname-names params)))))))
+      (org-number-sequence 0 (1- (length vars)))))))
+
 (defun org-babel-R-quote-tsv-field (s)
   "Quote field S for export to R."
   (if (stringp s)
@@ -139,23 +138,25 @@ This function is called by `org-babel-execute-src-block'."
 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
   "Construct R code assigning the elisp VALUE to a variable named NAME."
   (if (listp value)
-      (let ((transition-file (make-temp-file "org-babel-R-import")))
+      (let ((transition-file (org-babel-temp-file "R-import-")))
         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
         (unless (listp (car value)) (setq value (list value)))
-        (with-temp-file (org-babel-maybe-remote-file transition-file)
+        (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=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
-                name transition-file
+                name (org-babel-process-file-name transition-file 'noquote)
                 (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
                 (if rownames-p "1" "NULL")))
     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 
+(defvar ess-ask-for-ess-directory nil)
 (defun org-babel-R-initiate-session (session params)
   "If there is not a current R process then create one."
   (unless (string= session "none")
     (let ((session (or session "*R*"))
-          (ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))
+          (ess-ask-for-ess-directory
+           (and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
       (if (org-babel-comint-buffer-livep session)
           session
         (save-window-excursion
@@ -168,6 +169,15 @@ This function is called by `org-babel-execute-src-block'."
                (buffer-name))))
           (current-buffer))))))
 
+(defvar ess-local-process-name nil)
+(defun org-babel-R-associate-session (session)
+  "Associate R code buffer with an R session.
+Make SESSION be the inferior ESS process associated with the
+current code buffer."
+  (setq ess-local-process-name
+        (process-name (get-buffer-process session)))
+  (ess-make-buffer-current))
+
 (defun org-babel-R-construct-graphics-device-call (out-file params)
   "Construct the call to the graphics device."
   (let ((devices
@@ -205,65 +215,78 @@ This function is called by `org-babel-execute-src-block'."
 
 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
-(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
-write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
-(defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
+(defvar org-babel-R-write-object-command "{function(object, transfer.file) {invisible(if(inherits(try(write.table(object, file=transfer.file, sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE), silent=TRUE),\"try-error\")) {if(!file.exists(transfer.file)) file.create(transfer.file)})}}(object=%s, transfer.file=\"%s\")")
 
 (defun org-babel-R-evaluate
   (session body result-type column-names-p row-names-p)
-  "Pass BODY to the R process in SESSION.
-If RESULT-TYPE equals 'output then return a list of the outputs
-of the statements in BODY, if RESULT-TYPE equals 'value then
-return the value of the last statement in BODY, as elisp."
-  (if (not session)
-      ;; external process evaluation
-      (case result-type
-        (output (org-babel-eval org-babel-R-command body))
-        (value
-         (let ((tmp-file (make-temp-file "org-babel-R-results-")))
-           (org-babel-eval org-babel-R-command
-                           (format org-babel-R-wrapper-method
-                                   body tmp-file
-                                   (if row-names-p "TRUE" "FALSE")
-                                   (if column-names-p
-                                       (if row-names-p "NA" "TRUE")
-                                     "FALSE")))
-           (org-babel-R-process-value-result
-            (org-babel-import-elisp-from-file
-             (org-babel-maybe-remote-file tmp-file)) column-names-p))))
-    ;; comint session evaluation
-    (case result-type
-      (value
-       (let ((tmp-file (make-temp-file "org-babel-R"))
-             broke)
-         (org-babel-comint-with-output (session org-babel-R-eoe-output)
-           (insert (mapconcat
-                    #'org-babel-chomp
-                    (list
-                     body
-                     (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))  column-names-p)))
-      (output
-       (mapconcat
-        #'org-babel-chomp
-        (butlast
-         (delq nil
-               (mapcar
-                #'identity
-                (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)))) 2) "\n")))))
+  "Evaluate R code in BODY."
+  (if session
+      (org-babel-R-evaluate-session
+       session body result-type column-names-p row-names-p)
+    (org-babel-R-evaluate-external-process
+     body result-type column-names-p row-names-p)))
+
+(defun org-babel-R-evaluate-external-process
+  (body result-type column-names-p row-names-p)
+  "Evaluate BODY in external R process.
+If RESULT-TYPE equals 'output then return standard output as a
+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-")))
+       (org-babel-eval org-babel-R-command
+                       (format org-babel-R-write-object-command
+                               (if row-names-p "TRUE" "FALSE")
+                               (if column-names-p
+                                   (if row-names-p "NA" "TRUE")
+                                 "FALSE")
+                               (format "{function ()\n{\n%s\n}}()" body)
+                               (org-babel-process-file-name tmp-file 'noquote)))
+       (org-babel-R-process-value-result
+        (org-babel-import-elisp-from-file tmp-file '(16)) column-names-p)))
+    (output (org-babel-eval org-babel-R-command body))))
+
+(defun org-babel-R-evaluate-session
+  (session body result-type 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
+last statement in BODY, as elisp."
+  (case result-type
+    (value
+     (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 tmp-file
+        (format org-babel-R-write-object-command
+                (if row-names-p "TRUE" "FALSE")
+                (if column-names-p
+                    (if row-names-p "NA" "TRUE")
+                  "FALSE")
+                ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
+       (org-babel-R-process-value-result
+        (org-babel-import-elisp-from-file tmp-file '(16))  column-names-p)))
+    (output
+     (mapconcat
+      #'org-babel-chomp
+      (butlast
+       (delq nil
+             (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)))) 2) "\n"))))
 
 (defun org-babel-R-process-value-result (result column-names-p)
   "R-specific processing of return value.