lisp/essl-bug.el

   1 ;;; essl-bug.el -- ESS[BUGS]
   2 ;;;WARNING! deprecated; see essl-bugs.el, essd-bugs.el, essd-jags.el
   3
   4 ;; Copyright (C) 2001 Rodney Sparapani
   5 ;; Copyright (C) 2002--2004 Free Software Foundation, Inc.
   6 ;; Copyright (C) 2002--2004 A.J. Rossini, Rich M. Heiberger, Martin
   7 ;;      Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
   8
   9 ;; Original Author: Rodney Sparapani <rsparapa@mcw.edu>
  10 ;; Created: 27 February 2001
  11 ;; Maintainers: ESS-core <ESS-core@stat.math.ethz.ch>
  12
  13 ;; Keywords: BUGS, bugs, BACKBUGS, backbugs.
  14
  15 ;; This file is part of ESS
  16
  17 ;; This file is free software; you can redistribute it and/or modify
  18 ;; it under the terms of the GNU General Public License as published by
  19 ;; the Free Software Foundation; either version 2, or (at your option)
  20 ;; any later version.
  21 ;;
  22 ;; This file is distributed in the hope that it will be useful,
  23 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;; GNU General Public License for more details.
  26 ;;
  27 ;; You should have received a copy of the GNU General Public License
  28 ;; along with GNU Emacs; see the file COPYING.  If not, write to
  29 ;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
  30 ;;
  31 ;; In short: you may use this code any way you like, as long as you
  32 ;; don't charge money for it, remove this notice, or hold anyone liable
  33 ;; for its results.
  34
  35 ;; Code:
  36
  37 (require 'font-lock)
  38 (require 'comint)
  39 (require 'ess-emcs)
  40
  41 (if (assoc "\\.[bB][uUoO][gG]\\'" auto-mode-alist) nil
  42     (setq auto-mode-alist
  43         (append
  44            '(("\\.[bB][uUoO][gG]\\'"    . ess-bugs-mode)
  45              ("\\.[bB][mM][dD]\\'"      . ess-bugs-mode))
  46         auto-mode-alist)
  47     )
  48 )
  49
  50 (defgroup ess-bugs nil
  51   "ESS: BUGS."
  52   :group 'ess
  53   :prefix "ess-")
  54
  55 (defcustom ess-bugs-batch-method
  56   (if ess-microsoft-p
  57     (if (w32-shell-dos-semantics) 'ms-dos 'sh)
  58     (if (equal system-type 'Apple-Macintosh) 'apple-script 'sh))
  59   "Method used by `ess-bugs-batch'.
  60 The default is based on the value of the emacs variable `system-type'
  61 and, on Windows machines, the function `w32-shell-dos-semantics'.
  62 'ms-dos           if *shell* follows MS-DOS semantics
  63 'sh               if *shell* runs sh, ksh, csh, tcsh or bash
  64 'apple-script     *shell* unavailable, use AppleScript
  65
  66 Windows users running MS-DOS in *shell* will get 'ms-dos by default.
  67
  68 Windows users running bash in *shell* will get 'sh by default.
  69
  70 Unix users will get 'sh by default.
  71
  72 Users whose default is not 'sh, but are accessing a remote machine with
  73 `telnet', `rlogin', or `ssh', should have the following in ~/.emacs
  74    (setq-default ess-bugs-batch-method 'sh)"
  75     :group 'ess-bugs
  76 )
  77
  78 (defcustom ess-bugs-batch-version "0.6"
  79   "*ESS[BUGS]: The batch BUGS version to use."
  80     :group 'ess-bugs
  81     :type  'string
  82 )
  83
  84 ;; SJE Thu 13 May 2004
  85 ;; The "backbugs" scripts can be found in ess-etc-directory, so maybe we
  86 ;; can use ess-etc-directory here too.
  87 (defcustom ess-bugs-batch-command
  88     (if (equal ess-bugs-batch-version "0.6") "backbugs"
  89       (if (equal ess-bugs-batch-version "0.5") "backbug5"
  90         (if (equal ess-bugs-batch-version "jags") "jags" "backbugs")))
  91   "*ESS[BUGS]: The name of the command to run BUGS in batch mode.
  92
  93 Set to the name of the batch BUGS script that comes with ESS or
  94 to the name of BUGS command. Make sure it is in your PATH or
  95 add path to the command name."
  96     :group 'ess-bugs
  97     :type  'string
  98 )
  99
 100 (defcustom ess-bugs-batch-post-command
 101     (if (equal ess-bugs-batch-method 'sh) "&" " ")
 102     "*ESS[BUGS]: Modifiers at the end of the batch BUGS command line."
 103     :group 'ess-bugs
 104     :type  'string
 105 )
 106
 107 (defcustom ess-bugs-batch-pre-command
 108     (if (equal ess-bugs-batch-method 'sh) "test -f nohup.out && rm -f nohup.out || true; nohup"
 109         (if ess-microsoft-p "start"))
 110     "*ESS[BUGS]: Modifiers at the beginning of the batch BUGS command line."
 111     :group 'ess-bugs
 112     :type  'string
 113 )
 114
 115 (defcustom ess-bugs-default-bins (if (equal ess-bugs-batch-version "0.6") "32" " ")
 116 "ESS[BUGS]: Number of bins to use in the Griddy algorithm (Metropolis sampling)."
 117     :group 'ess-bugs
 118     :type  'string
 119 )
 120
 121 (defcustom ess-bugs-default-burn-in "500"
 122     "ESS[BUGS]: Burn-in iterations to discard."
 123     :group 'ess-bugs
 124     :type  'string
 125 )
 126
 127 (defcustom ess-bugs-default-update "1000"
 128     "ESS[BUGS]: Iterations to store."
 129     :group 'ess-bugs
 130     :type  'string
 131 )
 132
 133 (defcustom ess-bugs-default-checkpoint "100"
 134     "ESS[BUGS]: Make a snapshot every this many iterations."
 135     :group 'ess-bugs
 136     :type  'string
 137 )
 138
 139 (defvar ess-bugs-file "."
 140    "ESS[BUGS]: BUGS file with PATH.")
 141
 142 (defvar ess-bugs-file-root "."
 143    "ESS[BUGS]: Root of BUGS file.")
 144
 145 (defvar ess-bugs-file-suffix "."
 146    "ESS[BUGS]: Suffix of BUGS file.")
 147
 148 (defvar ess-bugs-file-dir "."
 149    "ESS[BUGS]: Directory of BUGS file.")
 150
 151 (defvar ess-bugs-file-data "..."
 152    "ESS[BUGS]: BUGS data file.")
 153
 154 (defcustom ess-bugs-inits-suffix ".in"
 155    "ESS[BUGS]: BUGS init file suffix."
 156     :group 'ess-bugs
 157     :type  'string
 158 )
 159
 160 (defcustom ess-bugs-data-suffix ".dat"
 161    "ESS[BUGS]: BUGS data file suffix."
 162     :group 'ess-bugs
 163     :type  'string
 164 )
 165
 166 (defcustom ess-bugs-suffix-regexp
 167     (concat "[.]\\([bB][oOuU][gG]\\|[bB][mM][dD]\\|"
 168         (if ess-bugs-inits-suffix (concat
 169             "\\|" (downcase ess-bugs-inits-suffix) "\\|" (upcase ess-bugs-inits-suffix)))
 170         (if ess-bugs-data-suffix (concat
 171             "\\|" (downcase ess-bugs-data-suffix) "\\|" (upcase ess-bugs-data-suffix)))
 172         "\\)")
 173     "*ESS[BUGS]: Regular expression for BUGS suffixes."
 174     :group 'ess-bugs
 175     :type  'string
 176 )
 177
 178 (defcustom ess-bugs-mode-hook nil
 179     "*ESS[BUGS]: List of functions to call upon entering mode."
 180     :group 'ess-bugs
 181     :type 'hook)
 182
 183 (defvar ess-bugs-monitor-vars " "
 184     "ESS[BUGS]: List of BUGS variables to be written out to a file.")
 185
 186 (defvar ess-bugs-stats-vars " "
 187     "ESS[BUGS]: List of BUGS variables to be summarized with statistics.")
 188
 189 (defvar ess-bugs-mode-map nil
 190    "ESS[BUGS]: Keymap for mode.")
 191
 192 (if ess-bugs-mode-map nil
 193     (setq ess-bugs-mode-map (make-keymap))
 194     (define-key ess-bugs-mode-map (quote [f2])  'ess-revert-wisely)
 195     (define-key ess-bugs-mode-map (quote [f12]) 'ess-bugs-next-action)
 196 )
 197
 198
 199 (defvar ess-bugs-syntax-table nil
 200    "ESS[BUGS]: Syntax table for mode.")
 201
 202 (if ess-bugs-syntax-table nil
 203     (setq ess-bugs-syntax-table (make-syntax-table))
 204     (modify-syntax-entry ?\\ "."  ess-bugs-syntax-table)
 205     (modify-syntax-entry ?#  "<"  ess-bugs-syntax-table)
 206     (modify-syntax-entry ?\n ">"  ess-bugs-syntax-table)
 207     (modify-syntax-entry ?(  "()" ess-bugs-syntax-table)
 208     (modify-syntax-entry ?)  ")(" ess-bugs-syntax-table)
 209     (modify-syntax-entry ?.  "w"  ess-bugs-syntax-table)
 210 )
 211
 212
 213 (defvar ess-bugs-font-lock-keywords
 214     (list
 215         ;; .bug files
 216         (cons "#.*\n"                   font-lock-comment-face)
 217
 218         (cons "^[ \t]*\\(const\\|data\\|in\\(it\\(ialize\\|s\\)\\)?\\|model\\|var\\)\\>"
 219                                         font-lock-keyword-face)
 220
 221         ;;(cons "\\<in[ \t]+[1-9]\\>"   font-lock-keyword-face)
 222
 223         (cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisqr\\|"
 224                 "dexp\\|dirch\\|exp\\|gamma\\|interval\\|lnorm\\|logis\\|"
 225                 "mnorm\\|multi\\|negbin\\|norm\\|par\\|pois\\|sum\\|"
 226                 "t\\|unif\\|weib\\|wish\\)[ \t\n]*(")
 227                                         font-lock-reference-face)
 228
 229         (cons (concat "\\<\\(for\\|cloglog\\|equals\\|exp\\|inprod\\|"
 230                 "inverse\\|log\\(det\\|fact\\|gam\\|it\\)?\\|max\\|"
 231                 "mean\\|min\\|phi\\|pow\\|probit\\|sd\\|sort\\|sqrt\\|"
 232                 "step\\|sum\\|I\\|T\\)[ \t\n]*(")
 233                                         font-lock-function-name-face)
 234
 235         ;; .bmd files
 236         (cons (concat "\\<\\(by\\|clear\\|chain\\|checkpoint\\|compile\\|data\\|"
 237                 "diag\\|help\\|inits\\|iter\\|model\\|monitor\\|"
 238                 "out\\|q\\|save\\|stats\\|stem\\|thin\\|update\\)[ \t\n]*(")
 239                                         font-lock-function-name-face)
 240
 241         (cons "^[ \t]*\\(clear\\|coda\\|exit\\|monitor\\|parameters\\|seed\\|set\\|to\\)\\>"
 242                                         font-lock-keyword-face)
 243
 244         ;; .dat files
 245         ;;(cons (concat "\\<\\(c\\|list\\)[ \t\n]*(")
 246         ;;                              font-lock-function-name-face)
 247     )
 248     "ESS[BUGS]: Font lock keywords."
 249 )
 250
 251
 252 (defun ess-bugs-file ()
 253 "ESS[BUGS]: Set internal variables dealing with BUGS files.
 254 Set `ess-bugs-file', `ess-bugs-file-root', `ess-bugs-file-suffix'
 255 and `ess-bugs-file-dir'."
 256    (let ((ess-bugs-temp-string (buffer-name)))
 257         (setq ess-bugs-file (expand-file-name ess-bugs-temp-string))
 258         (setq ess-bugs-file-dir
 259             (convert-standard-filename (file-name-directory ess-bugs-file)))
 260         (setq ess-bugs-file-root
 261             (file-name-nondirectory (file-name-sans-extension ess-bugs-file)))
 262
 263         (if (fboundp 'file-name-extension)
 264             (setq ess-bugs-file-suffix (file-name-extension ess-bugs-temp-string))
 265             ;;else
 266             (setq ess-bugs-file-suffix (car (last (split-string ess-bugs-temp-string "[.]")))))
 267
 268         (setq ess-bugs-file-suffix
 269             (downcase (car (split-string (concat "." ess-bugs-file-suffix) "[<]"))))
 270
 271         (setq ess-bugs-file (concat ess-bugs-file-dir ess-bugs-file-root ess-bugs-file-suffix))
 272    )
 273 )
 274
 275
 276 (defun ess-switch-to-suffix (suffix)
 277    "ESS: Switch to file with suffix."
 278    (find-file (concat ess-bugs-file-dir ess-bugs-file-root suffix))
 279
 280    (if (equal 0 (buffer-size)) (progn
 281         (if (equal ".bug" suffix) (progn
 282             (insert (concat "model %MODEL;\n"))
 283             (insert (concat "const N = 0;#%N\n"))
 284             (insert "var ;\n")
 285             (insert "#%MONITOR;\n")
 286             (insert "#%STATS;\n")
 287             (insert (concat "data  in \"%DATA\";\n"))
 288             (insert (concat "inits in \"%INITS\";\n"))
 289             (insert "{\n")
 290             (insert "    for (i in 1:N) {\n    \n")
 291             (insert "    }\n")
 292             (insert "}\n")
 293         ))
 294
 295         (if (equal ".bmd" suffix) (let
 296             ((tmp-bugs-file-dir (if (equal ess-bugs-batch-version "0.6") ess-bugs-file-dir)))
 297             (insert (concat "compile(\"" tmp-bugs-file-dir ess-bugs-file-root ".bug\")\n"))
 298             (insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in0\")\n"))
 299             (insert (concat "update(" ess-bugs-default-burn-in ")\n"))
 300             (insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in1\")\n"))
 301             (insert "#%MONITOR\n\n#%MONITOR\n")
 302             (if (equal ess-bugs-batch-version "0.6")
 303                 (insert (concat "checkpoint(" ess-bugs-default-checkpoint ")\n")))
 304             (insert (concat "update(" ess-bugs-default-update ")\n"))
 305             (insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in2\")\n"))
 306             (insert "#%STATS\n\n#%STATS\n")
 307             (insert "q()\n")
 308             ;;(insert "q(\"" ess-bugs-file-dir ess-bugs-file-root ".bog\")\n")
 309         ))
 310     ))
 311 )
 312
 313 (defun ess-exit-notify-sh (string)
 314   "Detect completion or failure of submitted job and notify the user."
 315   (let* ((exit-done "\\[[0-9]+\\]\\ *\\+*\\ *\\(Exit\\|Done\\).*$")
 316          (beg (string-match exit-done string)))
 317     (if beg (message (substring string beg (match-end 0))))))
 318
 319 (defun ess-bugs-next-action ()
 320    "ESS[BUGS]: Perform the appropriate next action."
 321    (interactive)
 322    (ess-bugs-file)
 323
 324    (if (equal ".bug" ess-bugs-file-suffix) (ess-bugs-na-bug))
 325    ;;else
 326    (if (equal ".bmd" ess-bugs-file-suffix) (ess-bugs-na-bmd))
 327 )
 328
 329 (defun ess-bugs-na-bmd ()
 330     "ESS[BUGS]: Perform the Next-Action for .bmd."
 331
 332     (save-buffer)
 333     (shell)
 334
 335     (if (w32-shell-dos-semantics)
 336         (if (string-equal ":" (substring ess-bugs-file 1 2))
 337             (progn
 338                 (insert (substring ess-bugs-file 0 2))
 339                 (comint-send-input)
 340             )
 341         )
 342     )
 343
 344         (insert (concat "cd \"" ess-bugs-file-dir "\""))
 345         (comint-send-input)
 346
 347         (insert (concat ess-bugs-batch-pre-command " " ess-bugs-batch-command " "
 348             (if (equal ess-bugs-batch-version "0.6") ess-bugs-default-bins)
 349              " " ess-bugs-file-root " "
 350             (if (equal ess-bugs-batch-version "0.6")
 351                  ess-bugs-file (concat ess-bugs-file-root ".bmd"))
 352              " " ess-bugs-batch-post-command))
 353
 354         (comint-send-input)
 355 )
 356
 357
 358 (defun ess-bugs-na-bug ()
 359     "ESS[BUGS]: Perform Next-Action for .bug"
 360
 361         (if (equal 0 (buffer-size)) (ess-switch-to-suffix ".bug")
 362             (save-excursion (let
 363                 ((tmp-bugs-file-dir (if (equal ess-bugs-batch-version "0.6") ess-bugs-file-dir)))
 364                 (goto-char (point-min))
 365
 366                 (if (search-forward "%MODEL" nil t)
 367                     (replace-match ess-bugs-file-root t t))
 368
 369                 (if (search-forward "%DATA" nil t) (progn
 370                     (setq ess-bugs-file-data
 371                         (concat tmp-bugs-file-dir ess-bugs-file-root ess-bugs-data-suffix))
 372                     (replace-match ess-bugs-file-data t t))
 373                 ;;else
 374                 (if (search-forward-regexp "data.+in[ \t\n]+\"\\(.*\\)\"" nil t)
 375                     (setq ess-bugs-file-data (match-string 1))
 376                 ;;else
 377                     (setq ess-bugs-file-data "...")
 378                 ))
 379
 380                 (if (search-forward "%INITS" nil t)
 381                     (replace-match
 382                         (concat tmp-bugs-file-dir ess-bugs-file-root ess-bugs-inits-suffix) t t))
 383
 384                 (let ((ess-bugs-temp-string " ")
 385                     (ess-bugs-buffer-ptr nil))
 386                     (goto-char (point-min))
 387
 388                     (if (search-forward-regexp
 389                             "N[ \t]*=[ \t]*[0-9]+[ \t]*;[ \t]*#[ \t]*%N" nil t) (progn
 390
 391                         (save-excursion (save-match-data
 392                             (setq ess-bugs-buffer-ptr (find-buffer-visiting ess-bugs-file-data))
 393
 394                             (if ess-bugs-buffer-ptr (set-buffer ess-bugs-buffer-ptr)
 395                                 (set-buffer (create-file-buffer ess-bugs-file-data))
 396                                 (insert-file-contents ess-bugs-file-data t))
 397
 398                             (setq ess-bugs-temp-string
 399                                 (concat "N = "
 400                                     (int-to-string (count-lines (point-min) (point-max))) ";#%N"))
 401                         ))
 402
 403                         (replace-match ess-bugs-temp-string t t)
 404                     ))
 405                 )
 406
 407                 (let (
 408                     (ess-bugs-search-min nil)
 409                     (ess-bugs-search-max nil)
 410                     (ess-bugs-search-vars
 411 "\\([a-zA-Z0-9.]+\\)\\(\\(\\[\\)[a-zA-Z0-9]*\\(,\\)?[a-zA-Z0-9]*\\(\\]\\)\\)?[ \t]*[,]?[ \t]*\\(#.*\\)?[\n]?"
 412                     ))
 413
 414                     (goto-char (point-min))
 415
 416                     (if (search-forward-regexp "%MONITOR[ \t]+" nil t)
 417                         (setq ess-bugs-search-min (point))
 418                     ;;else
 419                         (setq ess-bugs-search-min (search-forward "var"))
 420                     )
 421
 422                     (setq ess-bugs-search-max (search-forward-regexp ";"))
 423
 424                     (goto-char ess-bugs-search-min)
 425                     (setq ess-bugs-monitor-vars "")
 426
 427                     (while (search-forward-regexp ess-bugs-search-vars ess-bugs-search-max t)
 428
 429                         (setq ess-bugs-monitor-vars
 430                             (concat ess-bugs-monitor-vars "monitor("
 431                                 (match-string 1) (match-string 3) (match-string 4) (match-string 5) ")\n"))
 432                     )
 433
 434                     (setq ess-bugs-monitor-vars
 435                         (concat "#%MONITOR\n" ess-bugs-monitor-vars "#%MONITOR\n"))
 436
 437                     (goto-char (point-min))
 438
 439                     (if (search-forward-regexp "%STATS[ \t]+" nil t) (progn
 440                         (setq ess-bugs-search-min (point))
 441                         (setq ess-bugs-search-max (search-forward-regexp ";"))
 442
 443                         (goto-char ess-bugs-search-min)
 444                         (setq ess-bugs-stats-vars "")
 445
 446                         (while (search-forward-regexp ess-bugs-search-vars ess-bugs-search-max t)
 447
 448                             (setq ess-bugs-stats-vars
 449                                 (concat ess-bugs-stats-vars "stats("
 450                                     (match-string 1) (match-string 3) (match-string 4) (match-string 5) ")\n"))
 451                         )
 452
 453                         (setq ess-bugs-stats-vars (concat "#%STATS\n" ess-bugs-stats-vars "#%STATS\n"))
 454                     )
 455
 456 ;; replace-in-string may not be available, work-around necessary; see below
 457 ;;                      (setq ess-bugs-stats-vars
 458 ;;                          (replace-in-string ess-bugs-monitor-vars "#%MONITOR" "#%STATS"))
 459 ;;                      (setq ess-bugs-stats-vars
 460 ;;                          (replace-in-string ess-bugs-stats-vars "monitor" "stats" t))
 461
 462                     ;;else
 463                     (setq ess-bugs-stats-vars ess-bugs-monitor-vars)
 464
 465                     (while (string-match "#%MONITOR" ess-bugs-stats-vars)
 466                         (setq ess-bugs-stats-vars
 467                             (replace-match "#%STATS" t t ess-bugs-stats-vars)))
 468
 469                     (while (string-match "monitor" ess-bugs-stats-vars)
 470                         (setq ess-bugs-stats-vars
 471                             (replace-match "stats" t t ess-bugs-stats-vars)))
 472
 473                     )
 474                 )
 475
 476             ))
 477
 478             (save-buffer)
 479             (ess-switch-to-suffix ".bmd")
 480
 481     (save-excursion
 482         (goto-char (point-min))
 483
 484         (if (search-forward-regexp "#%MONITOR\\(.\\|\n\\)*#%MONITOR\n" nil t)
 485             (replace-match ess-bugs-monitor-vars t))
 486
 487         (if (search-forward-regexp "#%STATS\\(.\\|\n\\)*#%STATS\n" nil t)
 488             (replace-match ess-bugs-stats-vars t))
 489     )
 490
 491         )
 492 )
 493
 494
 495 (defun ess-bugs-mode ()
 496    "ESS[BUGS]: Major mode for Classic BUGS."
 497    (interactive)
 498    (kill-all-local-variables)
 499    (setq major-mode 'ess-bugs-mode)
 500    (setq mode-name "ESS[BUGS]")
 501    (use-local-map ess-bugs-mode-map)
 502    (setq font-lock-auto-fontify t)
 503    (make-local-variable 'font-lock-defaults)
 504    (setq font-lock-defaults '(ess-bugs-font-lock-keywords nil t))
 505    (run-hooks 'ess-bugs-mode-hook)
 506
 507    (if (not (w32-shell-dos-semantics))
 508         (add-hook 'comint-output-filter-functions 'ess-exit-notify-sh))
 509 )
 510
 511 (defun ess-bugs-sci-to-round-4-dp ()
 512     "ESS[BUGS]: round output from +/-0.000E+/-0 to 4 decimal places."
 513     (interactive)
 514     (setq buffer-read-only nil)
 515     (save-excursion (goto-char 0)
 516     (save-match-data (let ((ess-bugs-replacement-string nil)
 517                             (ess-bugs-replacement-9 0)
 518                             (ess-bugs-replacement-diff 0))
 519      (while (search-forward-regexp "-?[0-9][.][0-9][0-9][0-9]E[+-][0-9]" nil t)
 520             (setq ess-bugs-replacement-string
 521                   (int-to-string (string-to-number (match-string 0))))
 522             (setq ess-bugs-replacement-diff (- (match-end 0) (match-beginning 0)))
 523             (save-match-data
 524                 (setq ess-bugs-replacement-9
 525                     (string-match "99999999999$" ess-bugs-replacement-string))
 526
 527                 (if (not ess-bugs-replacement-9)
 528                     (setq ess-bugs-replacement-9
 529                         (string-match "000000000001$" ess-bugs-replacement-string))))
 530
 531             (if ess-bugs-replacement-9
 532                 (setq ess-bugs-replacement-string
 533                     (substring ess-bugs-replacement-string 0 ess-bugs-replacement-9)))
 534
 535             (setq ess-bugs-replacement-diff
 536                 (- ess-bugs-replacement-diff (string-width ess-bugs-replacement-string)))
 537
 538            (while (> ess-bugs-replacement-diff 0)
 539                 (setq ess-bugs-replacement-string (concat ess-bugs-replacement-string " "))
 540                 (setq ess-bugs-replacement-diff (- ess-bugs-replacement-diff 1)))
 541
 542            (replace-match ess-bugs-replacement-string))))))
 543
 544 ;;; ESS[BUGS-Shell] for running BUGS interactively
 545 (defgroup ess-bugs-shell nil
 546   "ESS: BUGS-Shell."
 547   :group 'ess-bugs
 548   :prefix "ess-")
 549
 550 (defcustom ess-bugs-shell-buffer-name "BUGS"
 551   "*ESS[BUGS-Shell]: The name of the BUGS-Shell buffer."
 552   :group 'ess-bugs-shell
 553   :type  'string)
 554
 555 (defcustom ess-bugs-shell-command "bugs"
 556   "*ESS[BUGS-Shell]: The name of the command to run BUGS interactively.
 557
 558 Set to the name of the batch BUGS script that comes with ESS or
 559 to the name of BUGS command. Make sure it is in your PATH or
 560 add path to the command name."
 561   :group 'ess-bugs-shell
 562   :type  'string)
 563
 564 (defcustom ess-bugs-shell-default-output-file-root "bugs"
 565   "*ESS[BUGS-Shell]: Default value for the root of output files."
 566   :group 'ess-bugs-shell
 567   :type  'string)
 568
 569 (defcustom ess-bugs-shell-mode-hook nil
 570   "*ESS[BUGS-Shell]: List of functions to call upon entering mode."
 571   :group 'ess-bugs-shell
 572   :type 'hook)
 573
 574 (defun ess-bugs-shell ()
 575   "Create a buffer with BUGS running as a subprocess."
 576   (interactive)
 577   (require 'shell)
 578   (switch-to-buffer (concat "*" ess-bugs-shell-buffer-name "*"))
 579   (make-comint ess-bugs-shell-buffer-name ess-bugs-shell-command nil
 580                ess-bugs-default-bins ess-bugs-shell-default-output-file-root)
 581   (comint-mode)
 582   (setq shell-dirtrackp t
 583         major-mode 'bugs-shell-mode
 584         mode-name "ESS[BUGS-Shell]"
 585         comint-prompt-regexp "^Bugs> *")
 586    (make-local-variable 'font-lock-defaults)
 587    (setq font-lock-defaults '(ess-bugs-font-lock-keywords nil t))
 588    (run-hooks 'ess-bugs-shell-mode-hook)
 589   )
 590
 591 (provide 'essl-bug)