lisp/essd-r.el

   1 ;;; essd-r.el --- R customization
   2
   3 ;; Copyright (C) 1997--2005 A.J. Rossini, Rich M. Heiberger, Martin
   4 ;;      Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
   5
   6 ;; Original Author: A.J. Rossini
   7 ;; Created: 12 Jun 1997
   8 ;; Maintainers: ESS-core <ESS-core@stat.math.ethz.ch>
   9
  10 ;; Keywords: start up, configuration.
  11
  12 ;; This file is part of ESS.
  13
  14 ;; This file is free software; you can redistribute it and/or modify
  15 ;; it under the terms of the GNU General Public License as published by
  16 ;; the Free Software Foundation; either version 2, or (at your option)
  17 ;; any later version.
  18
  19 ;; This file is distributed in the hope that it will be useful,
  20 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;; GNU General Public License for more details.
  23
  24 ;; You should have received a copy of the GNU General Public License
  25 ;; along with GNU Emacs; see the file COPYING.  If not, write to
  26 ;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
  27
  28 ;;; Commentary:
  29 ;;; This file defines all the R customizations for ESS.  See essl-s.el
  30 ;;; for general S language customizations.
  31
  32 ;;; Autoloads and Requires
  33
  34 (ess-message "[essd-r:] (require 'essl-s)")
  35 (require 'essl-s)
  36
  37 (require 'essd-r-args);  for now
  38
  39 ;; modify S Syntax table:
  40 (setq R-syntax-table S-syntax-table)
  41
  42 ;; In R 2.x, back tick now is a quote character, so lets tell Emacs
  43 ;; that it is; the problem below for older R should no longer be a
  44 ;; serious issue.
  45 ;;R >= 1.8: back tick `string` -- unfortunately no *pair* checking:
  46 ;; breaks when things like `..' are used:
  47 (modify-syntax-entry ?` "\"" R-syntax-table)
  48 (modify-syntax-entry ?_  "_"  R-syntax-table) ; foo_bar is symbol in R >=1.9
  49
  50 (ess-message "[essd-r:] (autoload ..) & (def** ..)")
  51
  52 (autoload 'inferior-ess "ess-inf" "Run an ESS process.")
  53 (autoload 'ess-mode     "ess-mode" "Edit an ESS process.")
  54
  55 ;;; Code:
  56
  57 (defvar R-customize-alist
  58   (append
  59    '((ess-local-customize-alist         . 'R-customize-alist)
  60      (ess-dialect                       . "R")
  61      (ess-suffix                        . "R")
  62      (ess-dump-filename-template        . (ess-replace-regexp-in-string
  63                                            "S$" ess-suffix ; in the one from custom:
  64                                            ess-dump-filename-template-proto))
  65      (ess-mode-syntax-table             . R-syntax-table)
  66      (ess-mode-editing-alist            . R-editing-alist)
  67      (ess-change-sp-regexp              . ess-R-change-sp-regexp)
  68      (ess-help-sec-regex                . ess-help-R-sec-regex)
  69      (ess-help-sec-keys-alist           . ess-help-R-sec-keys-alist)
  70      (ess-loop-timeout                  . ess-S-loop-timeout);fixme: dialect spec.
  71      (ess-cmd-delay                     . ess-R-cmd-delay)
  72      (ess-function-pattern              . ess-R-function-pattern)
  73      (ess-object-name-db-file           . "ess-r-namedb.el" )
  74      (ess-imenu-mode-function           . 'ess-imenu-R)
  75      (inferior-ess-program              . inferior-R-program-name)
  76      (inferior-ess-objects-command      . inferior-R-objects-command)
  77      (inferior-ess-font-lock-keywords   . inferior-ess-R-font-lock-keywords)
  78      (inferior-ess-search-list-command  . "search()\n")
  79      (inferior-ess-help-command         . "help(\"%s\", htmlhelp=FALSE)\n")
  80      (inferior-ess-help-filetype        . nil)
  81      (inferior-ess-exit-command         . "q()")
  82      (inferior-ess-exit-prompt          . "Save workspace image? [y/n/c]: ")
  83      (inferior-ess-primary-prompt       . "\\([A-Z][][A-Za-z0-9.]*\\)*> ")
  84      (inferior-ess-secondary-prompt     . "+ ?")
  85      ;;harmful for shell-mode's C-a: -- but "necessary" for ESS-help?
  86      (inferior-ess-start-file           . nil) ;; "~/.ess-R"
  87      (inferior-ess-start-args           . "")
  88      (ess-STERM         . "iESS")
  89      (ess-editor        . R-editor)
  90      (ess-pager         . R-pager)
  91      )
  92    S-common-cust-alist)
  93   "Variables to customize for R -- set up later than emacs initialization.")
  94
  95 (defvar ess-r-versions '("R-1" "R-2" "R-devel" "R-patched")
  96   "List of partial strings for versions of R to access within ESS.
  97 Each string specifies the start of a filename.  If a filename
  98 beginning with one of these strings is found on `exec-path', a M-x
  99 command for that version of R is made available.  For example, if the
 100 file \"R-1.8.1\" is found and this variable includes the string
 101 \"R-1\", a function called `M-x R-1.8.1' will be available to run that
 102 version of R.
 103 If duplicate versions of the same program are found (which happens if
 104 the same path is listed on `exec-path' more than once), they are
 105 ignored by calling `ess-uniq-list'.
 106 Set this variable to nil to disable searching for other versions of R.
 107 If you set this variable, you need to restart Emacs (and set this variable
 108 before ess-site is loaded) for it to take effect.")
 109
 110 ;;;### autoload
 111 (defun R (&optional start-args)
 112   "Call 'R', the 'GNU S' system from the R Foundation.
 113 Optional prefix (C-u) allows to set command line arguments, such as
 114 --vsize.  This should be OS agnostic.
 115 If you have certain command line arguments that should always be passed
 116 to R, put them in the variable `inferior-R-args'."
 117   (interactive "P")
 118   (setq ess-customize-alist R-customize-alist)
 119   (ess-write-to-dribble-buffer   ;; for debugging only
 120    (format
 121     "\n(R): ess-dialect=%s, buf=%s, start-arg=%s\n current-prefix-arg=%s\n"
 122     ess-dialect (current-buffer) start-args current-prefix-arg))
 123   (let* ((r-always-arg
 124           (if (or ess-microsoft-p (eq system-type 'cygwin))
 125               "--ess "
 126             "--no-readline "))
 127          (r-start-args
 128           (concat r-always-arg
 129                   inferior-R-args " " ; add space just in case
 130                   (if start-args
 131                       (read-string
 132                        (concat "Starting Args [other than `"
 133                                r-always-arg
 134                                "'] ? "))
 135                     nil)))
 136          ;;Micro$ ?: default-process-coding-system ;-breaks UTF locales on Unix:
 137          )
 138     (if ess-microsoft-p
 139         (setq default-process-coding-system '(undecided-dos . undecided-dos)))
 140     (inferior-ess r-start-args) ;; (R)
 141     (ess-write-to-dribble-buffer
 142      (format "(R): inferior-ess-language-start=%s\n"
 143              inferior-ess-language-start))
 144     ;; currently rely on baseenv() which is in R only since version 2.2:
 145     (ess-eval-linewise
 146      "if(!exists(\"baseenv\", mode=\"function\")) baseenv <- function() NULL"
 147      nil nil nil 'wait-prompt);; solving "lines running together"
 148     (if inferior-ess-language-start
 149         (ess-eval-linewise inferior-ess-language-start
 150                            nil nil nil 'wait-prompt))))
 151
 152 ;;;### autoload
 153 (defun R-mode  (&optional proc-name)
 154   "Major mode for editing R source.  See `ess-mode' for more help."
 155   (interactive)
 156   (setq ess-customize-alist R-customize-alist)
 157   ;;(setq imenu-generic-expression R-imenu-generic-expression)
 158   (ess-mode R-customize-alist proc-name)
 159   (if (fboundp 'ess-add-toolbar) (ess-add-toolbar))
 160   ;; ECB needs seminatic stuff.
 161   ;;  (if (featurep 'semantic)
 162   ;;      (setq semantic-toplevel-bovine-table r-toplevel-bovine-table))
 163   (if ess-imenu-use-S
 164       (progn (require 'ess-menu)
 165              (ess-imenu-R)))
 166   ;; MM:      ^^^^^^^^^^^ should really use ess-imenu-mode-function from the
 167   ;;     alist above!
 168   )
 169
 170
 171 (fset 'r-mode 'R-mode)
 172
 173 (defun ess-r-versions-create ()
 174   "Generate the `M-x R-X.Y' functions for starting other versions of R.
 175 See `ess-r-versions' for strings that determine which functions are created.
 176
 177 The local variable `ess-r-versions-created' is used to return list of
 178 the new R defuns, if any, that were created.  The defuns will normally
 179 be placed on the menubar upon ESS initialisation."
 180
 181
 182   (if (not ess-r-versions)
 183       nil                               ;nothing to return
 184     ;; else, if ess-r-versions is non-nil, let's try to find those R versions.
 185     ;; This works by creating a temp buffer where the template function is
 186     ;; edited so that X.Y is replaced by the version name
 187     (let ((template "")
 188           (beg)
 189           (versions)
 190           (version)
 191           (eval-buf (get-buffer-create "*ess-temp-r-evals*"))
 192           (ess-r-versions-created)
 193           )
 194       ;; This is the template function used for creating M-x R-X.Y.
 195       (setq template "(defun R-X.Y (&optional start-args)
 196   \"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS.
 197 This function was generated by `ess-r-versions-create'.\"
 198   (interactive \"P\")
 199   (let ((inferior-R-program-name \"R-X.Y\"))
 200     (R start-args)))
 201
 202 ")
 203       (save-excursion
 204         (set-buffer eval-buf)
 205         ;; clear the buffer.
 206         (delete-region (point-min) (point-max))
 207
 208         ;; Find which versions of R we want.  Remove the pathname, leaving just
 209         ;; the name of the executable.
 210         (setq versions
 211               (ess-uniq-list
 212                (mapcar 'file-name-nondirectory
 213                        (apply 'nconc
 214                               (mapcar 'ess-find-exec-completions
 215                                       ess-r-versions)))))
 216         (ess-write-to-dribble-buffer
 217          (format "(R): ess-r-versions-create making M-x defuns for %s"
 218                  (mapconcat 'identity versions " ")))
 219         (setq ess-r-versions-created versions) ;keep copy for returning at end.
 220         ;; Iterate over each string in VERSIONS, creating a new defun each time.
 221         (while versions
 222           (setq version (car versions)
 223                 versions (cdr versions))
 224           (setq beg (point))
 225           (insert template)
 226           (goto-char beg)
 227           (while (search-forward "R-X.Y" nil t)
 228             (replace-match version t t))
 229           (goto-char (point-max))
 230           )
 231         ;; buffer has now been created with defuns, so eval them!
 232         (eval-buffer)
 233         (kill-buffer eval-buf)
 234         )
 235       ess-r-versions-created)))
 236
 237
 238
 239
 240 ;; (ess-r-version-date "R-1.9")
 241 (defun ess-r-version-date (rver)
 242   "Return the date of the version of R named RVER.
 243 The date is returned as a date string.  If the version of R could
 244 not be found from the output of the RVER program, \"-1\" is
 245 returned."
 246   (let (ver-string
 247         (date "-1"))
 248     (setq ver-string (shell-command-to-string
 249                       (concat rver " --version")))
 250     (when (string-match "R version [^\n\(]+ (\\([0-9-]+\\))"  ver-string)
 251       (setq date (match-string 1 ver-string)))
 252     (cons  date rver)))
 253
 254 (defun ess-newest-r (rvers)
 255   "Check all the versions of RVERS to see which is the newest.
 256 Create an alias for that version of R, so that M-x R-newest will run it."
 257   (let ( rnewest
 258          (rtimes (mapcar 'ess-r-version-date rvers)))
 259     (setq rnewest (ess-find-newest-date rtimes))
 260     (fset 'R-newest (intern rnewest))
 261     ;; SJE: 2007-07-13 -- following line is a temp var to check that
 262     ;; the newest version of R is found correctly.
 263     (setq temp-ess-newest rtimes)
 264     (message (concat "newest is " rnewest))))
 265
 266
 267 ;; Test case for following defun:
 268 ;; (setq a '( ("2003-10-04" . "R-1.7")
 269 ;;         ("2006-11-19" . "R-2.2")
 270 ;;         ("2007-07-01" . "R-dev")
 271 ;;         ("-1" . "R-broken")
 272 ;;         ("2005-12-30" . "R-2.0")))
 273 ;; (ess-find-newest-date a)
 274 (defun ess-find-newest-date (rvers)
 275   "Find the newest version of R given in the a-list RVERS.
 276 Each element of RVERS is a dotted pair (date . R-version), where
 277 date is given as e.g.\"2007-11-30\" so that we can compare dates
 278 as strings.  If a date is listed as \"-1\", that version of R
 279 could not be found.
 280
 281 If the value returned is nil, no valid newest version of R could be found."
 282   (let (new-r
 283         (new-time "0"))
 284     (while rvers
 285       (setq this-r (car rvers)
 286             rvers (cdr rvers))
 287       (when (string< new-time (car this-r))
 288         (setq new-time (car this-r)
 289               new-r    (cdr this-r))))
 290     new-r))
 291
 292
 293 (defun ess-find-rterm (&optional ess-R-root-dir)
 294   "Find the full path of all occurences of Rterm.exe under the ESS-R-ROOT-DIR.
 295 If ESS-R-ROOT-DIR is nil, construct it by looking for an occurence of Rterm.exe
 296 in the exec-path.  If there are no occurences of Rterm.exe in the exec-path,
 297 then use \"c:/progra~1/R/\" which is the default location for the R distribution."
 298   (let* ((Rpath)
 299   (rwxxyy)
 300   (rw)
 301   (Rterm nil))
 302     (if (not ess-R-root-dir)
 303  (progn
 304    (setq Rpath (executable-find "Rterm"))
 305    (setq ess-R-root-dir
 306   (if Rpath
 307       (expand-file-name
 308        (concat
 309         (file-name-directory Rpath)
 310         "../../"))
 311     "c:/progra~1/R/"))))
 312     (setq rwxxyy (append (file-name-all-completions "rw" ess-R-root-dir)
 313     (file-name-all-completions "R-1" ess-R-root-dir)
 314     (file-name-all-completions "R-2" ess-R-root-dir)
 315     (file-name-all-completions "R-devel" ess-R-root-dir)
 316     (file-name-all-completions "R-patched" ess-R-root-dir)
 317 ))  ;; this needs to rewritten to use (append '("rw") ess-r-versions)
 318     (while rwxxyy
 319       (setq rw (car rwxxyy))
 320       (setq rwxxyy (cdr rwxxyy))
 321       (setq Rterm (cons (ess-replace-regexp-in-string "[\\]" "/"
 322                             (concat ess-R-root-dir rw "bin/Rterm.exe"))
 323                   Rterm)))
 324     Rterm))
 325
 326 (defun ess-rterm-versions-create ()
 327   "Generate the `M-x rwxxyy' functions for starting other versions of R.
 328 See `ess-rterm-versions' for strings that determine which functions
 329 are created.
 330
 331 The result `ess-rterm-versions-created' will store a list of the new
 332 Rterm defuns, if any, that were created.  The defuns will normally be
 333 placed on the menubar upon ESS initialisation."
 334
 335   ;; This works by creating a temp buffer where the template function is
 336   ;; edited so that R-X.Y is replaced by the version name
 337   (let ((template "")
 338         (beg)
 339         (versions)
 340         (version)
 341         (version-root)
 342         (eval-buf (get-buffer-create "*ess-temp-r-evals*"))
 343         (ess-rterm-versions-created)
 344 )
 345     ;;
 346     ;; This is the template function used for creating M-x R-X.Y.
 347     (setq template "(defun R-X.Y (&optional start-args)
 348   \"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS.
 349 This function was generated by `ess-rterm-versions-create'.\"
 350   (interactive \"P\")
 351   (let ((inferior-R-program-name \"Rterm-X.Y\"))
 352     (R start-args)))
 353
 354 ")
 355     (save-excursion
 356       (set-buffer eval-buf)
 357       ;; clear the buffer.
 358       (delete-region (point-min) (point-max))
 359
 360       ;; Find which versions of R we want.  Remove the pathname, leaving just
 361       ;; the name of the executable.
 362       (setq versions ess-rterm-versions)
 363       (ess-write-to-dribble-buffer
 364        (format "(R): ess-rterm-versions-create making M-x defuns for %s"
 365                (mapconcat 'identity versions " ")))
 366
 367       ;; Iterate over each string in VERSIONS, creating a new defun each time.
 368       (while versions
 369         (setq version (car versions)
 370               versions (cdr versions)
 371               version-root (file-name-nondirectory
 372                             (substring (file-name-directory
 373                                         (substring
 374                                          (file-name-directory version)
 375                                          0 -1))
 376                                        0 -1)))
 377         (setq beg (point))
 378         (insert template)
 379         (goto-char beg)
 380         (while (search-forward "R-X.Y" nil t)
 381           (replace-match version-root t t))
 382         (goto-char beg)
 383         (while (search-forward "Rterm-X.Y" nil t)
 384           (replace-match version t t))
 385         (goto-char (point-max))
 386         (setq ess-rterm-versions-created
 387               (cons version-root ess-rterm-versions-created))
 388         )
 389       ;; buffer has now been created with defuns, so eval them!
 390       (eval-buffer)
 391       (kill-buffer eval-buf)
 392       )
 393     ess-rterm-versions-created))
 394
 395 ;;;### autoload
 396 (defun Rnw-mode ()
 397   "Major mode for editing Sweave(R) source.
 398 See `noweb-mode' and `R-mode' for more help."
 399   (interactive)
 400   (require 'ess-noweb);; << probably someplace else
 401   (noweb-mode 1); turn it on
 402   (noweb-set-doc-mode 'latex-mode)
 403   (noweb-set-code-mode 'R-mode)
 404   (run-hooks 'Rnw-mode-hook))
 405
 406 (fset 'Snw-mode 'Rnw-mode); just a synonym (for now or ever)
 407
 408
 409 (autoload 'ess-transcript-mode "ess-trns"
 410   "Major mode for editing S transcript files." t)
 411
 412 (defun R-transcript-mode ()
 413   "Does the right thing."
 414   (interactive)
 415   (ess-transcript-mode R-customize-alist))
 416
 417 (fset 'r-transcript-mode 'R-transcript-mode)
 418
 419 (defun R-fix-T-F (&optional from quietly)
 420   "Fix T/F into TRUE and FALSE *cautiously*, i.e. not in comments and strings;
 421  starting from the current position (point)."
 422   (interactive "d\nP"); point and prefix (C-u)
 423   (save-excursion
 424     (goto-char from)
 425     (ess-rep-regexp "\\(\\([][=,()]\\|<-\\|_\\) *\\)T\\>" "\\1TRUE"
 426                     'fixcase nil (not quietly))
 427     (goto-char from)
 428     (ess-rep-regexp "\\(\\([][=,()]\\|<-\\|_\\\) *\\)F\\>" "\\1FALSE"
 429                     'fixcase nil (not quietly))))
 430
 431 ;; From: Sebastian Luque <spluque@gmail.com>
 432 ;; To: ess-help@stat.math.ethz.ch
 433 ;; Date: Mon, 01 May 2006 19:17:49 -0500
 434
 435 ;; Without knowing how to tell R to use w3m from within Emacs, and after
 436 ;; switching to Konqueror's window for the millionth time, I wrote the
 437 ;; following function:
 438
 439 ;; This emulates some of the functionality of RSiteSearch() and tests ok in
 440 ;; my system GNU Emacs 22.0.50.1 (i486-pc-linux-gnu, X toolkit, Xaw3d scroll
 441 ;; bars) of 2006-04-27 on pacem, modified by Debian.  This has the benefit of
 442 ;; displaying results with whatever you've told browse-url to use; in my
 443 ;; case, w3m with the emacs-w3m package.
 444
 445 ;; My elisp skills are rather poor, so comments and suggestions for
 446 ;; improvement are welcome.
 447 ;; --
 448 ;; Seb
 449
 450
 451 ;; MM _FIXME_: This only works correctly for  Emacs 22.0.50 (alpha)
 452 ;;             for 21.x it has problems in the (completing-read-multiple .)
 453 ;;             at the end
 454 (defun R-site-search (string)
 455   "Search the R archives for STRING, using default criteria.  If
 456 called with a prefix, options are available for
 457   1) matches per page,
 458   2) sections of the archives to search (separated by value of `crm-default-separator'),
 459   3) for displaying results in long or short formats, and
 460   4) for sorting by any given field.
 461 Completion is available for supplying options."
 462   (interactive "sSearch string: ")
 463   (let ((site "http://search.r-project.org/cgi-bin/namazu.cgi?query=")
 464         (okstring (replace-regexp-in-string " +" "+" string)))
 465     (if current-prefix-arg
 466         (let ((mpp (concat
 467                     "&max="
 468                     (completing-read
 469                      "Matches per page: "
 470                      '(("20" 1) ("30" 2) ("40" 3) ("50" 4) ("100" 5)))))
 471               (format (concat
 472                        "&result="
 473                        (completing-read
 474                         "Format: " '("normal" "short")
 475                         nil t "normal" nil "normal")))
 476               (sortby (concat
 477                        "&sort="
 478                        (completing-read
 479                         "Sort by: "
 480                         '(("score" 1) ("date:late" 2) ("date:early" 3)
 481                           ("field:subject:ascending" 4)
 482                           ("field:subject:decending" 5)
 483                           ("field:from:ascending" 6) ("field:from:decending" 7)
 484                           ("field:size:ascending" 8) ("field:size:decending" 9))
 485                         nil t "score" nil "score")))
 486               (restrict (concat
 487                          "&idxname="
 488                          (mapconcat
 489                           'identity
 490                           (completing-read-multiple
 491                            "Limit search to: "
 492                            '(("Rhelp02a" 1) ("functions" 2) ("docs" 3)
 493                              ("Rhelp01" 4))
 494                            nil t "Rhelp02a,functions,docs" nil
 495                            "Rhelp02a,functions,docs") "&idxname="))))
 496           (browse-url (concat site okstring mpp format sortby restrict)))
 497       ;; else: without prefix use defaults:
 498       (browse-url (concat site okstring "&max=20&result=normal&sort=score"
 499                           "&idxname=Rhelp02a&idxname=functions&idxname=docs")))))
 500
 501
 502 \f ; provides
 503
 504 (provide 'essd-r)
 505
 506 \f ; Local variables section
 507
 508 ;;; This file is automatically placed in Outline minor mode.
 509 ;;; The file is structured as follows:
 510 ;;; Chapters:     ^L ;
 511 ;;; Sections:    ;;*;;
 512 ;;; Subsections: ;;;*;;;
 513 ;;; Components:  defuns, defvars, defconsts
 514 ;;;              Random code beginning with a ;;;;* comment
 515
 516 ;;; Local variables:
 517 ;;; mode: emacs-lisp
 518 ;;; outline-minor-mode: nil
 519 ;;; mode: outline-minor
 520 ;;; outline-regexp: "\^L\\|\\`;\\|;;\\*\\|;;;\\*\\|(def[cvu]\\|(setq\\|;;;;\\*"
 521 ;;; End:
 522
 523 ;;; essd-r.el ends here