Merge from trunk

1 files changed, 67 insertions, 24 deletions

diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el
index 49a8a85cf6d..3dedb393654 100644
--- a/lisp/org/ob-R.el
+++ b/lisp/org/ob-R.el
@@ -39,24 +39,48 @@
 (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
-          res type family title fonts version paper encoding
-          pagecentre colormodel useDingbats horizontal)
+(declare-function org-remove-if-not "org" (predicate seq))
+
+(defconst org-babel-header-args:R
+  '((width               . :any)
+    (height              . :any)
+    (bg                  . :any)
+    (units               . :any)
+    (pointsize           . :any)
+    (antialias           . :any)
+    (quality             . :any)
+    (compression         . :any)
+    (res                 . :any)
+    (type                . :any)
+    (family              . :any)
+    (title               . :any)
+    (fonts               . :any)
+    (version             . :any)
+    (paper               . :any)
+    (encoding            . :any)
+    (pagecentre          . :any)
+    (colormodel          . :any)
+    (useDingbats         . :any)
+    (horizontal          . :any)
+    (results             . ((file list vector table scalar verbatim)
+                            (raw org html latex code pp wrap)
+                            (replace silent append prepend)
+                            (output value graphics))))
   "R-specific header arguments.")
 
 (defvar org-babel-default-header-args:R '())
 
-(defvar org-babel-R-command "R --slave --no-save"
-  "Name of command to use for executing R code.")
+(defcustom org-babel-R-command "R --slave --no-save"
+  "Name of command to use for executing R code."
+  :group 'org-babel
+  :version "24.1"
+  :type 'string)
 
-(defvar ess-local-process-name)
+(defvar ess-local-process-name) ; dynamically scoped
 (defun org-babel-edit-prep:R (info)
   (let ((session (cdr (assoc :session (nth 2 info)))))
     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
-      (save-match-data (org-babel-R-initiate-session session nil))
-      (setq ess-local-process-name (match-string 1 session)))))
+      (save-match-data (org-babel-R-initiate-session session nil)))))
 
 (defun org-babel-expand-body:R (body params &optional graphics-file)
   "Expand BODY according to PARAMS, return the expanded body."
@@ -120,7 +144,7 @@ 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"
+  "Return list of R statements assigning the block's variables."
   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
     (mapcar
      (lambda (pair)
@@ -146,25 +170,45 @@ 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 (org-babel-temp-file "R-import-")))
+      (let ((max (apply #'max (mapcar #'length (org-remove-if-not
+                                                #'sequencep value))))
+            (min (apply #'min (mapcar #'length (org-remove-if-not
+                                                #'sequencep value))))
+            (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 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 (org-babel-process-file-name transition-file 'noquote)
-                (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
-                (if rownames-p "1" "NULL")))
+          (insert
+           (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
+           "\n"))
+        (let ((file (org-babel-process-file-name transition-file 'noquote))
+              (header (if (or (eq (nth 1 value) 'hline) colnames-p)
+                          "TRUE" "FALSE"))
+              (row-names (if rownames-p "1" "NULL")))
+          (if (= max min)
+              (format "%s <- read.table(\"%s\",
+                      header=%s,
+                      row.names=%s,
+                      sep=\"\\t\",
+                      as.is=TRUE)" name file header row-names)
+            (format "%s <- read.table(\"%s\",
+                   header=%s,
+                   row.names=%s,
+                   sep=\"\\t\",
+                   as.is=TRUE,
+                   fill=TRUE,
+                   col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
+                    name file header row-names max))))
     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 
-(defvar ess-ask-for-ess-directory nil)
+(defvar ess-ask-for-ess-directory) ; dynamically scoped
 (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
-           (and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
+           (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
+                (not (cdr (assoc :dir params))))))
       (if (org-babel-comint-buffer-livep session)
           session
         (save-window-excursion
@@ -177,7 +221,6 @@ 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
@@ -219,7 +262,7 @@ current code buffer."
     (setq args (mapconcat
                 (lambda (pair)
                   (if (member (car pair) allowed-args)
-                      (format ",%s=%s"
+                      (format ",%s=%S"
                               (substring (symbol-name (car pair)) 1)
                               (cdr pair)) ""))
                 params ""))
@@ -245,7 +288,7 @@ current code buffer."
   (body result-type result-params 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
+string.  If RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (case result-type
     (value
@@ -272,7 +315,7 @@ last statement in BODY, as elisp."
   (session body result-type result-params 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
+string.  If RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (case result-type
     (value