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[ess.git] / lisp / essd-r.el

;;; essd-r.el --- R customization

;; Copyright (C) 1997--2005 A.J. Rossini, Rich M. Heiberger, Martin
;;      Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.

;; Original Author: A.J. Rossini
;; Created: 12 Jun 1997
;; Maintainers: ESS-core <ESS-core@stat.math.ethz.ch>

;; Keywords: start up, configuration.

;; This file is part of ESS.

;; This file 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 2, or (at your option)
;; any later version.

;; This file 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; see the file COPYING.  If not, write to
;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.

;;; Commentary:
;;; This file defines all the R customizations for ESS.  See essl-s.el
;;; for general S language customizations.

;;; Autoloads and Requires

(ess-message "[essd-r:] (require 'essl-s)")
(require 'essl-s)

(require 'essd-r-args);  for now

;; modify S Syntax table:
(setq R-syntax-table S-syntax-table)

;; In R 2.x, back tick now is a quote character, so lets tell Emacs
;; that it is; the problem below for older R should no longer be a
;; serious issue.
;;R >= 1.8: back tick `string` -- unfortunately no *pair* checking:
;; breaks when things like `..' are used:
(modify-syntax-entry ?` "\"" R-syntax-table)
(modify-syntax-entry ?_  "_"  R-syntax-table) ; foo_bar is symbol in R >=1.9

(ess-message "[essd-r:] (autoload ..) & (def** ..)")

(autoload 'inferior-ess "ess-inf" "Run an ESS process.")
(autoload 'ess-mode     "ess-mode" "Edit an ESS process.")

;;; Code:

(defvar R-customize-alist
  (append
   '((ess-local-customize-alist         . 'R-customize-alist)
     (ess-dialect                       . "R")
     (ess-suffix                        . "R")
     (ess-dump-filename-template        . (ess-replace-regexp-in-string
                                           "S$" ess-suffix ; in the one from custom:
                                           ess-dump-filename-template-proto))
     (ess-mode-syntax-table             . R-syntax-table)
     (ess-mode-editing-alist            . R-editing-alist)
     (ess-change-sp-regexp              . ess-R-change-sp-regexp)
     (ess-help-sec-regex                . ess-help-R-sec-regex)
     (ess-help-sec-keys-alist           . ess-help-R-sec-keys-alist)
     (ess-loop-timeout                  . ess-S-loop-timeout);fixme: dialect spec.
     (ess-cmd-delay                     . ess-R-cmd-delay)
     (ess-function-pattern              . ess-R-function-pattern)
     (ess-object-name-db-file           . "ess-r-namedb.el" )
     (ess-imenu-mode-function           . 'ess-imenu-R)
     (inferior-ess-program              . inferior-R-program-name)
     (inferior-ess-objects-command      . inferior-R-objects-command)
     (inferior-ess-font-lock-keywords   . inferior-ess-R-font-lock-keywords)
     (inferior-ess-search-list-command  . "search()\n")
     (inferior-ess-help-command         . "help(\"%s\", htmlhelp=FALSE)\n")
     (inferior-ess-help-filetype        . nil)
     (inferior-ess-exit-command         . "q()")
     (inferior-ess-exit-prompt          . "Save workspace image? [y/n/c]: ")
     (inferior-ess-primary-prompt       . "\\([A-Z][][A-Za-z0-9.]*\\)*> ")
     (inferior-ess-secondary-prompt     . "+ ?")
     ;;harmful for shell-mode's C-a: -- but "necessary" for ESS-help?
     (inferior-ess-start-file           . nil) ;; "~/.ess-R"
     (inferior-ess-start-args           . "")
     (ess-STERM         . "iESS")
     (ess-editor        . R-editor)
     (ess-pager         . R-pager)
     )
   S-common-cust-alist)
  "Variables to customize for R -- set up later than emacs initialization.")

(defvar ess-r-versions '("R-1" "R-2" "R-devel" "R-patched")
  "List of partial strings for versions of R to access within ESS.
Each string specifies the start of a filename.  If a filename
beginning with one of these strings is found on `exec-path', a M-x
command for that version of R is made available.  For example, if the
file \"R-1.8.1\" is found and this variable includes the string
\"R-1\", a function called `M-x R-1.8.1' will be available to run that
version of R.
If duplicate versions of the same program are found (which happens if
the same path is listed on `exec-path' more than once), they are
ignored by calling `ess-uniq-list'.
Set this variable to nil to disable searching for other versions of R.
If you set this variable, you need to restart Emacs (and set this variable
before ess-site is loaded) for it to take effect.")

;;;### autoload
(defun R (&optional start-args)
  "Call 'R', the 'GNU S' system from the R Foundation.
Optional prefix (C-u) allows to set command line arguments, such as
--vsize.  This should be OS agnostic.
If you have certain command line arguments that should always be passed
to R, put them in the variable `inferior-R-args'."
  (interactive "P")
  (setq ess-customize-alist R-customize-alist)
  (ess-write-to-dribble-buffer   ;; for debugging only
   (format
    "\n(R): ess-dialect=%s, buf=%s, start-arg=%s\n current-prefix-arg=%s\n"
    ess-dialect (current-buffer) start-args current-prefix-arg))
  (let* ((r-always-arg
          (if (or ess-microsoft-p (eq system-type 'cygwin))
              "--ess "
            "--no-readline "))
         (r-start-args
          (concat r-always-arg
                  inferior-R-args " " ; add space just in case
                  (if start-args
                      (read-string
                       (concat "Starting Args [other than `"
                               r-always-arg
                               "'] ? "))
                    nil)))
         ;;Micro$ ?: default-process-coding-system ;-breaks UTF locales on Unix:
         )
    (if ess-microsoft-p
        (setq default-process-coding-system '(undecided-dos . undecided-dos)))
    (inferior-ess r-start-args) ;; (R)
    (ess-write-to-dribble-buffer
     (format "(R): inferior-ess-language-start=%s\n"
             inferior-ess-language-start))
    ;; currently rely on baseenv() which is in R only since version 2.2:
    (ess-eval-linewise
     "if(!exists(\"baseenv\", mode=\"function\")) baseenv <- function() NULL"
     nil nil nil 'wait-prompt);; solving "lines running together"
    (if inferior-ess-language-start
        (ess-eval-linewise inferior-ess-language-start
                           nil nil nil 'wait-prompt))))

;;;### autoload
(defun R-mode  (&optional proc-name)
  "Major mode for editing R source.  See `ess-mode' for more help."
  (interactive)
  (setq ess-customize-alist R-customize-alist)
  ;;(setq imenu-generic-expression R-imenu-generic-expression)
  (ess-mode R-customize-alist proc-name)
  (if (fboundp 'ess-add-toolbar) (ess-add-toolbar))
  ;; ECB needs seminatic stuff.
  ;;  (if (featurep 'semantic)
  ;;      (setq semantic-toplevel-bovine-table r-toplevel-bovine-table))
  (if ess-imenu-use-S
      (progn (require 'ess-menu)
             (ess-imenu-R)))
  ;; MM:      ^^^^^^^^^^^ should really use ess-imenu-mode-function from the
  ;;     alist above!
  )


(fset 'r-mode 'R-mode)

;; FIXME: below we have a "copy-paste" version of this,
;; ess-rterm-versions-create  {which should really be merged into here}
(defun ess-r-versions-create ()
  "Generate the `M-x R-X.Y' functions for starting other versions of R.
See `ess-r-versions' for strings that determine which functions are created.

The local variable `ess-r-versions-created' is used to return list of
the new R defuns, if any, that were created.  The defuns will normally
be placed on the menubar upon ESS initialisation."

  (if (not ess-r-versions)
      nil                               ;nothing to return
    ;; else, if ess-r-versions is non-nil, let's try to find those R versions.
    ;; This works by creating a temp buffer where the template function is
    ;; edited so that X.Y is replaced by the version name
    (let ((template "")
          (beg)
          (versions)
          (version)
          (eval-buf (get-buffer-create "*ess-temp-r-evals*"))
          (ess-r-versions-created)
          )
      ;; This is the template function used for creating M-x R-X.Y.
      (setq template "(defun R-X.Y (&optional start-args)
  \"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS.
This function was generated by `ess-r-versions-create'.\"
  (interactive \"P\")
  (let ((inferior-R-program-name \"R-X.Y\"))
    (R start-args)))

")
      (save-excursion
        (set-buffer eval-buf)
        ;; clear the buffer.
        (delete-region (point-min) (point-max))

        ;; Find which versions of R we want.  Remove the pathname, leaving just
        ;; the name of the executable.
        (setq versions
              (ess-uniq-list
               (mapcar 'file-name-nondirectory
                       (apply 'nconc
                              (mapcar 'ess-find-exec-completions
                                      ess-r-versions)))))
        (ess-write-to-dribble-buffer
         (format "(R): ess-r-versions-create making M-x defuns for %s"
                 (mapconcat 'identity versions " ")))
        (setq ess-r-versions-created versions) ;keep copy for returning at end.
        ;; Iterate over each string in VERSIONS, creating a new defun each time.
        (while versions
          (setq version (car versions)
                versions (cdr versions))
          (setq beg (point))
          (insert template)
          (goto-char beg)
          (while (search-forward "R-X.Y" nil t)
            (replace-match version t t))
          (goto-char (point-max))
          )
        ;; buffer has now been created with defuns, so eval them!
        (eval-buffer)
        (kill-buffer eval-buf)
        )
      ess-r-versions-created)))


;; (ess-r-version-date "R-2.5.1") (ess-r-version-date "R-patched")
;; (ess-r-version-date "R-1.2.1") (ess-r-version-date "R-1.8.1")
;; Note that for R-devel, ver-string is something like
;; R version 2.6.0 Under development (unstable) (2007-07-14 r42234)
;; Antique examples are 'R 1.0.1  (April 14, 2000)' or 'R 1.5.1 (2002-06-17).'
(defun ess-r-version-date (rver)
  "Return the date of the version of R named RVER.
The date is returned as a date string.  If the version of R could
not be found from the output of the RVER program, \"-1\" is
returned."
  (let (ver-string
        (date "-1"))
    (setq ver-string (shell-command-to-string
                      (concat rver " --version")))
    (when (string-match 
           "R \\(version \\)?[1-9][^\n]+ (\\(2[0-9-]+\\)\\( r[0-9]+\\)?)"
           ver-string)
      (setq date (match-string 2 ver-string)))
    (cons  date rver)))

(defun ess-newest-r (rvers)
  "Check all the versions of RVERS to see which is the newest.
Create an alias for that version of R, so that M-x R-newest will run it."
  (let* ((rtimes (mapcar 'ess-r-version-date rvers))
         (rnewest (ess-find-newest-date rtimes)))

    (fset 'R-newest 
          (intern
           (if ess-microsoft-p
               (file-name-nondirectory
                (substring (file-name-directory
                            (substring (file-name-directory rnewest) 0 -1))
                           0 -1))
             rnewest)))
    ;; SJE: 2007-07-13 -- following line is a temp var to check that
    ;; the newest version of R is found correctly.
    (setq temp-ess-newest rtimes)
    (message (concat "newest is " rnewest))))


;; Test case for following defun:
;; (setq a '( ("2003-10-04" . "R-1.7")
;;         ("2006-11-19" . "R-2.2")
;;         ("2007-07-01" . "R-dev")
;;         ("-1" . "R-broken")
;;         ("2005-12-30" . "R-2.0")))
;; (ess-find-newest-date a)
(defun ess-find-newest-date (rvers)
  "Find the newest version of R given in the a-list RVERS.
Each element of RVERS is a dotted pair (date . R-version), where
date is given as e.g.\"2007-11-30\" so that we can compare dates
as strings.  If a date is listed as \"-1\", that version of R
could not be found.

If the value returned is nil, no valid newest version of R could be found."
  (let (new-r this-r
        (new-time "0"))
    (while rvers
      (setq this-r (car rvers)
            rvers (cdr rvers))
      (when (string< new-time (car this-r))
        (setq new-time (car this-r)
              new-r    (cdr this-r))))
    new-r))


(defun ess-find-rterm (&optional ess-R-root-dir)
  "Find the full path of all occurences of Rterm.exe under the ESS-R-ROOT-DIR.
If ESS-R-ROOT-DIR is nil, construct it by looking for an occurence of Rterm.exe
in the exec-path.  If there are no occurences of Rterm.exe in the exec-path,
then use \"c:/progra~1/R/\" which is the default location for the R distribution."
  (let* ((Rpath)
  (rwxxyy)
  (rw)
  (Rterm nil))
    (if (not ess-R-root-dir)
 (progn
   (setq Rpath (executable-find "Rterm"))
   (setq ess-R-root-dir
  (if Rpath
      (expand-file-name
       (concat
        (file-name-directory Rpath)
        "../../"))
    "c:/progra~1/R/"))))
    (setq rwxxyy (append (file-name-all-completions "rw" ess-R-root-dir)
    (file-name-all-completions "R-1" ess-R-root-dir)
    (file-name-all-completions "R-2" ess-R-root-dir)
    (file-name-all-completions "R-devel" ess-R-root-dir)
    (file-name-all-completions "R-patched" ess-R-root-dir)
))  ;; this needs to rewritten to use (append '("rw") ess-r-versions)
    (while rwxxyy
      (setq rw (car rwxxyy))
      (setq rwxxyy (cdr rwxxyy))
      (setq Rterm (cons (ess-replace-regexp-in-string "[\\]" "/"
                            (concat ess-R-root-dir rw "bin/Rterm.exe"))
                  Rterm)))
    Rterm))

(defun ess-rterm-versions-create ()
  "Generate the `M-x rwxxyy' functions for starting other versions of R.
See `ess-rterm-versions' for strings that determine which functions
are created.

The result `ess-rterm-versions-created' will store a list of the new
Rterm defuns, if any, that were created.  The defuns will normally be
placed on the menubar upon ESS initialisation."

  ;; This works by creating a temp buffer where the template function is
  ;; edited so that R-X.Y is replaced by the version name
  (let ((template "")
        (beg)
        (versions)
        (version)
        (version-root)
        (eval-buf (get-buffer-create "*ess-temp-r-evals*"))
        (ess-rterm-versions-created)
)
    ;;
    ;; This is the template function used for creating M-x R-X.Y.
    (setq template "(defun R-X.Y (&optional start-args)
  \"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS.
This function was generated by `ess-rterm-versions-create'.\"
  (interactive \"P\")
  (let ((inferior-R-program-name \"Rterm-X.Y\"))
    (R start-args)))

")
    (save-excursion
      (set-buffer eval-buf)
      ;; clear the buffer.
      (delete-region (point-min) (point-max))

      ;; Find which versions of R we want.  Remove the pathname, leaving just
      ;; the name of the executable.
      (setq versions ess-rterm-versions)
      (ess-write-to-dribble-buffer
       (format "(R): ess-rterm-versions-create making M-x defuns for %s"
               (mapconcat 'identity versions " ")))

      ;; Iterate over each string in VERSIONS, creating a new defun each time.
      (while versions
        (setq version (car versions)
              versions (cdr versions)
              version-root (file-name-nondirectory
                            (substring (file-name-directory
                                        (substring
                                         (file-name-directory version)
                                         0 -1))
                                       0 -1)))
        (setq beg (point))
        (insert template)
        (goto-char beg)
        (while (search-forward "R-X.Y" nil t)
          (replace-match version-root t t))
        (goto-char beg)
        (while (search-forward "Rterm-X.Y" nil t)
          (replace-match version t t))
        (goto-char (point-max))
        (setq ess-rterm-versions-created
              (cons version-root ess-rterm-versions-created))
        )
      ;; buffer has now been created with defuns, so eval them!
      (eval-buffer)
      (kill-buffer eval-buf)
      )
    ess-rterm-versions-created))

;;;### autoload
(defun Rnw-mode ()
  "Major mode for editing Sweave(R) source.
See `noweb-mode' and `R-mode' for more help."
  (interactive)
  (require 'ess-noweb);; << probably someplace else
  (noweb-mode 1); turn it on
  (noweb-set-doc-mode 'latex-mode)
  (noweb-set-code-mode 'R-mode)
  (run-hooks 'Rnw-mode-hook))

(fset 'Snw-mode 'Rnw-mode); just a synonym (for now or ever)


(autoload 'ess-transcript-mode "ess-trns"
  "Major mode for editing S transcript files." t)

(defun R-transcript-mode ()
  "Does the right thing."
  (interactive)
  (ess-transcript-mode R-customize-alist))

(fset 'r-transcript-mode 'R-transcript-mode)

(defun R-fix-T-F (&optional from quietly)
  "Fix T/F into TRUE and FALSE *cautiously*, i.e. not in comments and strings;
 starting from the current position (point)."
  (interactive "d\nP"); point and prefix (C-u)
  (save-excursion
    (goto-char from)
    (ess-rep-regexp "\\(\\([][=,()]\\|<-\\|_\\) *\\)T\\>" "\\1TRUE"
                    'fixcase nil (not quietly))
    (goto-char from)
    (ess-rep-regexp "\\(\\([][=,()]\\|<-\\|_\\\) *\\)F\\>" "\\1FALSE"
                    'fixcase nil (not quietly))))

;; From: Sebastian Luque <spluque@gmail.com>
;; To: ess-help@stat.math.ethz.ch
;; Date: Mon, 01 May 2006 19:17:49 -0500

;; Without knowing how to tell R to use w3m from within Emacs, and after
;; switching to Konqueror's window for the millionth time, I wrote the
;; following function:

;; This emulates some of the functionality of RSiteSearch() and tests ok in
;; my system GNU Emacs 22.0.50.1 (i486-pc-linux-gnu, X toolkit, Xaw3d scroll
;; bars) of 2006-04-27 on pacem, modified by Debian.  This has the benefit of
;; displaying results with whatever you've told browse-url to use; in my
;; case, w3m with the emacs-w3m package.

;; My elisp skills are rather poor, so comments and suggestions for
;; improvement are welcome.
;; --
;; Seb


;; MM _FIXME_: This only works correctly for  Emacs 22.0.50 (alpha)
;;             for 21.x it has problems in the (completing-read-multiple .)
;;             at the end
(defun R-site-search (string)
  "Search the R archives for STRING, using default criteria.  If
called with a prefix, options are available for
  1) matches per page,
  2) sections of the archives to search (separated by value of `crm-default-separator'),
  3) for displaying results in long or short formats, and
  4) for sorting by any given field.
Completion is available for supplying options."
  (interactive "sSearch string: ")
  (let ((site "http://search.r-project.org/cgi-bin/namazu.cgi?query=")
        (okstring (replace-regexp-in-string " +" "+" string)))
    (if current-prefix-arg
        (let ((mpp (concat
                    "&max="
                    (completing-read
                     "Matches per page: "
                     '(("20" 1) ("30" 2) ("40" 3) ("50" 4) ("100" 5)))))
              (format (concat
                       "&result="
                       (completing-read
                        "Format: " '("normal" "short")
                        nil t "normal" nil "normal")))
              (sortby (concat
                       "&sort="
                       (completing-read
                        "Sort by: "
                        '(("score" 1) ("date:late" 2) ("date:early" 3)
                          ("field:subject:ascending" 4)
                          ("field:subject:decending" 5)
                          ("field:from:ascending" 6) ("field:from:decending" 7)
                          ("field:size:ascending" 8) ("field:size:decending" 9))
                        nil t "score" nil "score")))
              (restrict (concat
                         "&idxname="
                         (mapconcat
                          'identity
                          (completing-read-multiple
                           "Limit search to: "
                           '(("Rhelp02a" 1) ("functions" 2) ("docs" 3)
                             ("Rhelp01" 4))
                           nil t "Rhelp02a,functions,docs" nil
                           "Rhelp02a,functions,docs") "&idxname="))))
          (browse-url (concat site okstring mpp format sortby restrict)))
      ;; else: without prefix use defaults:
      (browse-url (concat site okstring "&max=20&result=normal&sort=score"
                          "&idxname=Rhelp02a&idxname=functions&idxname=docs")))))


\f ; provides

(provide 'essd-r)

\f ; Local variables section

;;; This file is automatically placed in Outline minor mode.
;;; The file is structured as follows:
;;; Chapters:     ^L ;
;;; Sections:    ;;*;;
;;; Subsections: ;;;*;;;
;;; Components:  defuns, defvars, defconsts
;;;              Random code beginning with a ;;;;* comment

;;; Local variables:
;;; mode: emacs-lisp
;;; outline-minor-mode: nil
;;; mode: outline-minor
;;; outline-regexp: "\^L\\|\\`;\\|;;\\*\\|;;;\\*\\|(def[cvu]\\|(setq\\|;;;;\\*"
;;; End:

;;; essd-r.el ends here