view lisp/org/ob-R.el @ 110410:f2e111723c3a

Merge changes made in Gnus trunk. Reimplement nnimap, and do tweaks to the rest of the code to support that. * gnus-int.el (gnus-finish-retrieve-group-infos) (gnus-retrieve-group-data-early): New functions. * gnus-range.el (gnus-range-nconcat): New function. * gnus-start.el (gnus-get-unread-articles): Support early retrieval of data. (gnus-read-active-for-groups): Support finishing the early retrieval of data. * gnus-sum.el (gnus-summary-move-article): Pass the move-to group name if the move is internal, so that nnimap can do fast internal moves. * gnus.el (gnus-article-special-mark-lists): Add uid/active tuples, for nnimap usage. * nnimap.el: Rewritten. * nnmail.el (nnmail-inhibit-default-split-group): New internal variable to allow the mail splitting to not return a default group. This is useful for nnimap, which will leave unmatched mail in the inbox. * utf7.el (utf7-encode): Autoload. Implement shell connection. * nnimap.el (nnimap-open-shell-stream): New function. (nnimap-open-connection): Use it. Get the number of lines by using BODYSTRUCTURE. (nnimap-transform-headers): Get the number of lines in each message. (nnimap-retrieve-headers): Query for BODYSTRUCTURE so that we get the number of lines. Not all servers return UIDNEXT. Work past this problem. Remove junk from end of file. Fix typo in "bogus" section. Make capabilties be case-insensitive. Require cl when compiling. Don't bug out if the LIST command doesn't have any parameters. 2010-09-17 Knut Anders Hatlen <[e-mail]> (tiny change) * nnimap.el (nnimap-get-groups): Don't bug out if the LIST command doesn't have any parameters. (mm-text-html-renderer): Document gnus-article-html. 2010-09-17 Julien Danjou <[e-mail]> (tiny fix) * mm-decode.el (mm-text-html-renderer): Document gnus-article-html. * dgnushack.el: Define netrc-credentials. If the user doesn't have a /etc/services, supply some sensible port defaults. Have `unseen-or-unread' select an unread unseen article first. (nntp-open-server): Return whether the open was successful or not. Throughout all files, replace (save-excursion (set-buffer ...)) with (with-current-buffer ... ). Save result so that it doesn't say "failed" all the time. Add ~/.authinfo to the default, since that's probably most useful for users. Don't use the "finish" method when we're reading from the agent. Add some more nnimap-relevant agent stuff to nnagent.el. * nnimap.el (nnimap-with-process-buffer): Removed. Revert one line that was changed by mistake in the last checkin. (nnimap-open-connection): Don't error out when we can't make a connection nnimap-related changes to avoid bugging out if we can't contact a server. * gnus-start.el (gnus-get-unread-articles): Don't try to scan groups from methods that are denied. * nnimap.el (nnimap-possibly-change-group): Return nil if we can't log in. (nnimap-finish-retrieve-group-infos): Make sure we're not waiting for nothing. * gnus-sum.el (gnus-select-newsgroup): Indent.

;;; ob-R.el --- org-babel functions for R code evaluation

;; Copyright (C) 2009, 2010  Free Software Foundation, Inc.

;; Author: Eric Schulte, Dan Davison
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: http://orgmode.org
;; Version: 7.01

;; This file is part of GNU Emacs.

;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.

;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.

;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.

;;; Commentary:

;; Org-Babel support for evaluating R code

;;; Code:
(require 'ob)
(require 'ob-ref)
(require 'ob-comint)
(require 'ob-eval)
(eval-when-compile (require 'cl))

(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" ())

(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)
  "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.")

(defun org-babel-expand-body:R (body params &optional processed-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
     ((lambda (inside)
	(if out-file
	    (append
	     (list (org-babel-R-construct-graphics-device-call out-file params))
	     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")))

(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))
           (session (org-babel-R-initiate-session
		     (first processed-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))
	   (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))
	     (or (equal "yes" rownames-p)
		 (org-babel-pick-name (nth 5 processed-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)))
    (org-babel-comint-in-buffer session
      (mapc (lambda (var)
              (end-of-line 1) (insert var) (comint-send-input nil t)
              (org-babel-comint-wait-for-output session)) var-lines))
    session))

(defun org-babel-load-session:R (session body params)
  "Load BODY into SESSION."
  (save-window-excursion
    (let ((buffer (org-babel-prep-session:R session params)))
      (with-current-buffer buffer
        (goto-char (process-mark (get-buffer-process (current-buffer))))
        (insert (org-babel-chomp body)))
      buffer)))

;; helper functions

(defun org-babel-R-quote-tsv-field (s)
  "Quote field S for export to R."
  (if (stringp s)
      (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
    (format "%S" s)))

(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")))
        ;; 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)
          (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
		(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))))

(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)))))
      (if (org-babel-comint-buffer-livep session)
	  session
	(save-window-excursion
	  (require 'ess) (R)
	  (rename-buffer
	   (if (bufferp session)
	       (buffer-name session)
	     (if (stringp session)
		 session
	       (buffer-name))))
	  (current-buffer))))))

(defun org-babel-R-construct-graphics-device-call (out-file params)
  "Construct the call to the graphics device."
  (let ((devices
	 '((:bmp . "bmp")
	   (:jpg . "jpeg")
	   (:jpeg . "jpeg")
	   (:tiff . "tiff")
	   (:png . "png")
	   (:svg . "svg")
	   (:pdf . "pdf")
	   (:ps . "postscript")
	   (:postscript . "postscript")))
	(allowed-args '(:width :height :bg :units :pointsize
			       :antialias :quality :compression :res
			       :type :family :title :fonts :version
			       :paper :encoding :pagecentre :colormodel
			       :useDingbats :horizontal))
	(device (and (string-match ".+\\.\\([^.]+\\)" out-file)
		     (match-string 1 out-file)))
	(extra-args (cdr (assq :R-dev-args params))) filearg args)
    (setq device (or (and device (cdr (assq (intern (concat ":" device))
					    devices))) "png"))
    (setq filearg
	  (if (member device '("pdf" "postscript" "svg")) "file" "filename"))
    (setq args (mapconcat
		(lambda (pair)
		  (if (member (car pair) allowed-args)
		      (format ",%s=%s"
			      (substring (symbol-name (car pair)) 1)
			      (cdr pair)) ""))
		params ""))
    (format "%s(%s=\"%s\"%s%s%s)"
	    device filearg out-file args
	    (if extra-args "," "") (or extra-args ""))))

(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)")

(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")))))

(defun org-babel-R-process-value-result (result column-names-p)
  "R-specific processing of return value.
Insert hline if column names in output have been requested."
  (if column-names-p
      (cons (car result) (cons 'hline (cdr result)))
    result))

(provide 'ob-R)

;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237

;;; ob-R.el ends here