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296 lines
16 KiB
296 lines
16 KiB
;;; ess-bugs-d.el --- ESS[BUGS] dialect -*- lexical-binding: t; -*-
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;; Copyright (C) 2008-2011 Rodney Sparapani
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;; Author: Rodney Sparapani
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;; Created: 13 March 2008
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;; Maintainer: ESS-help <ess-help@r-project.org>
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;; This file is part of ESS
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;; This file is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 2, or (at your option)
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;; any later version.
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;;
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;; This file is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; A copy of the GNU General Public License is available at
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;; https://www.r-project.org/Licenses/
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;;; Code:
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(require 'ess-bugs-l)
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(require 'ess-utils)
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(require 'ess-inf)
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(require 'ess-mode)
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(defvar ess-bugs-command "OpenBUGS" "Default BUGS program in PATH.")
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(make-local-variable 'ess-bugs-command)
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(defvar ess-bugs-monitor '("") "Default list of variables to monitor.")
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(make-local-variable 'ess-bugs-monitor)
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(defvar ess-bugs-thin 1 "Default thinning parameter.")
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(make-local-variable 'ess-bugs-thin)
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(defvar ess-bugs-chains 1 "Default number of chains.")
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(make-local-variable 'ess-bugs-chains)
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(defvar ess-bugs-burnin 10000 "Default burn-in.")
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(make-local-variable 'ess-bugs-burnin)
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(defvar ess-bugs-update 10000 "Default number of updates after burnin.")
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(make-local-variable 'ess-bugs-update)
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(defvar ess-bugs-system nil "Default whether BUGS recognizes the system command.")
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(defvar ess-bugs-font-lock-keywords
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(list
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;; .bug files
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(cons "#.*\n" font-lock-comment-face)
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(cons "^[ \t]*\\(model\\|var\\)\\>"
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font-lock-keyword-face)
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(cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisq\\|"
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"dexp\\|dirch\\|exp\\|\\(gen[.]\\)?gamma\\|hyper\\|"
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"interval\\|lnorm\\|logis\\|mnorm\\|mt\\|multi\\|"
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"negbin\\|norm\\(mix\\)?\\|par\\|pois\\|sum\\|t\\|"
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"unif\\|weib\\|wish\\)[ \t\n]*(")
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font-lock-constant-face)
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(cons (concat "\\<\\(abs\\|cos\\|C\\|dim\\|\\(i\\)?cloglog\\|equals\\|"
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"exp\\|for\\|inprod\\|interp[.]line\\|inverse\\|length\\|"
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"\\(i\\)?logit\\|logdet\\|logfact\\|loggam\\|max\\|mean\\|"
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"mexp\\|min\\|phi\\|pow\\|probit\\|prod\\|rank\\|round\\|"
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"sd\\|sin\\|sort\\|sqrt\\|step\\|sum\\|t\\|trunc\\|T\\)[ \t\n]*(")
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font-lock-function-name-face)
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;; .bmd files
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(cons (concat (regexp-opt '(
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"dicClear" "dicSet" "dicStats"
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"infoMemory" "infoModules" "infoNodeMethods"
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"infoNodeTypes" "infoNodeValues"
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"infoUpdatersbyDepth" "infoUpdatersbyName"
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"modelCheck" "modelCompile" "modelData"
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"modelDisable" "modelEnable" "modelGenInits"
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"modelInits" "modelPrecision" "modelQuit"
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"modelSaveState" "modelSetAP" "modelSetIts"
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"modelSetOR" "modelSetRN" "modelUpdate"
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"ranksClear" "ranksSet" "ranksStats"
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"samplesAutoC" "samplesBgr" "samplesCoda"
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"samplesDensity" "samplesHistory" "samplesSet"
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"sampleStats" "samplesThin"
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"summaryClear" "summarySet" "summaryStats"
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) 'words) "(")
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font-lock-function-name-face)
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(cons (concat (regexp-opt '("Local Variables" "End") 'words) ":")
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font-lock-keyword-face)
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)
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"ESS[BUGS]: Font lock keywords."
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)
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(defun ess-bugs-switch-to-suffix (suffix &optional bugs-chains bugs-monitor bugs-thin
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bugs-burnin bugs-update)
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"ESS[BUGS]: Switch to file with suffix."
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(find-file (concat ess-bugs-file-dir ess-bugs-file-root suffix))
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(if (equal 0 (buffer-size)) (progn
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(if (equal ".bug" suffix) (progn
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;(insert "var ;\n")
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(insert "model {\n")
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(insert " for (i in 1:N) {\n \n")
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(insert " }\n")
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(insert "}\n")
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(insert "#Local Variables" ":\n")
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; (insert "#enable-local-variables: :all\n")
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(insert "#ess-bugs-chains:1\n")
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(insert "#ess-bugs-monitor:(\"\")\n")
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(insert "#ess-bugs-thin:1\n")
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(insert "#ess-bugs-burnin:10000\n")
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(insert "#ess-bugs-update:10000\n")
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(insert "#End:\n")
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))
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(if (equal ".bmd" suffix) (let
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((ess-bugs-temp-chains "") (ess-bugs-temp-monitor ""))
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(if bugs-chains (setq ess-bugs-chains bugs-chains))
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(if bugs-monitor (setq ess-bugs-monitor bugs-monitor))
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(if bugs-thin (setq ess-bugs-thin bugs-thin))
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(setq ess-bugs-temp-chains
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(concat "modelCompile(" (format "%d" ess-bugs-chains) ")\n"))
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(setq bugs-chains ess-bugs-chains)
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(while (< 0 bugs-chains)
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(setq ess-bugs-temp-chains
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(concat ess-bugs-temp-chains
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"modelInits('" ess-bugs-file-root
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".##" (format "%d" bugs-chains) "', "
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(format "%d" bugs-chains) ")\n"))
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(setq bugs-chains (- bugs-chains 1)))
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(setq ess-bugs-temp-monitor "")
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(while (and (listp ess-bugs-monitor) (consp ess-bugs-monitor))
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(if (not (string-equal "" (car ess-bugs-monitor)))
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(setq ess-bugs-temp-monitor
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(concat ess-bugs-temp-monitor "samplesSet('"
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(car ess-bugs-monitor)
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;", thin(" (format "%d" ess-bugs-thin)
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"')\n")))
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(setq ess-bugs-monitor (cdr ess-bugs-monitor)))
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(insert "modelCheck('" ess-bugs-file-root ".bug')\n")
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(insert "modelData('" ess-bugs-file-root ".bdt')\n")
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(insert (ess-replace-in-string ess-bugs-temp-chains "##" "in"))
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(insert "modelGenInits()\n")
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(insert "modelUpdate(" (format "%d" bugs-burnin) ")\n")
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;(insert "modelUpdate(" (format "%d" (* bugs-thin bugs-burnin)) ")\n")
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(insert ess-bugs-temp-monitor)
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(insert "modelUpdate(" (format "%d" (* bugs-thin bugs-update)) ")\n")
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; (insert (ess-replace-in-string
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; (ess-replace-in-string ess-bugs-temp-chains
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; "modelCompile([0-9]+)" "#") "##" "to"))
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(if (< 1 bugs-thin) (insert "samplesThin(" (format "%d" bugs-thin) ")\n"))
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(insert "samplesCoda('*', '" ess-bugs-file-root "')\n")
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; (if ess-bugs-system (progn
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; (insert "system rm -f " ess-bugs-file-root ".ind\n")
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; (insert "system ln -s " ess-bugs-file-root "index.txt " ess-bugs-file-root ".ind\n")
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; (setq bugs-chains ess-bugs-chains)
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; (while (< 0 bugs-chains)
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; (setq ess-bugs-temp-chain (format "%d" bugs-chains))
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; ;.txt not recognized by BOA and impractical to over-ride
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; (insert "system rm -f " ess-bugs-file-root ess-bugs-temp-chain ".out\n")
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; (insert "system ln -s " ess-bugs-file-root "chain" ess-bugs-temp-chain ".txt "
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; ess-bugs-file-root ess-bugs-temp-chain ".out\n")
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; (setq bugs-chains (- bugs-chains 1)))))
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(insert "modelQuit()\n")
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(insert "Local Variables" ":\n")
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; (insert "enable-local-variables: :all\n")
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(insert "ess-bugs-chains:" (format "%d" ess-bugs-chains) "\n")
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(insert "ess-bugs-command:\"" ess-bugs-command "\"\n")
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(insert "End:\n")
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))
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))
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)
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(defun ess-bugs-na-bmd (bugs-command)
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"ESS[BUGS]: Perform the Next-Action for .bmd."
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;(ess-save-and-set-local-variables)
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(if (equal 0 (buffer-size)) (ess-bugs-switch-to-suffix ".bmd")
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;else
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(shell)
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(ess-sleep)
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(when (and (when (fboundp 'w32-shell-dos-semantics)
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(w32-shell-dos-semantics))
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(string-equal ":" (substring ess-bugs-file 1 2)))
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(insert (substring ess-bugs-file 0 2)))
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(comint-send-input)
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(insert "cd \"" ess-bugs-file-dir "\"")
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(comint-send-input)
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; (let ((ess-bugs-temp-chains ""))
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;
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; (while (< 0 bugs-chains)
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; (setq ess-bugs-temp-chains
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; (concat (format "%d " bugs-chains) ess-bugs-temp-chains))
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; (setq bugs-chains (- bugs-chains 1)))
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;; (insert "echo '"
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;; ess-bugs-batch-pre-command " " bugs-command " < "
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;; ess-bugs-file-root ".bmd > " ess-bugs-file-root ".bog 2>&1 "
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;; ess-bugs-batch-post-command "' > " ess-bugs-file-root ".bsh")
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;; (comint-send-input)
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;; (insert "at -f " ess-bugs-file-root ".bsh now")
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;; (comint-send-input)
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(insert "echo '"
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ess-bugs-batch-pre-command " " bugs-command " < "
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ess-bugs-file-root ".bmd > " ess-bugs-file-root ".bog 2>&1 "
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ess-bugs-batch-post-command "' | at now")
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(comint-send-input)
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))
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(defun ess-bugs-na-bug ()
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"ESS[BUGS]: Perform Next-Action for .bug"
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(if (equal 0 (buffer-size)) (ess-bugs-switch-to-suffix ".bug")
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;else
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(ess-save-and-set-local-variables)
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(ess-bugs-switch-to-suffix ".bmd"
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ess-bugs-chains ess-bugs-monitor ess-bugs-thin ess-bugs-burnin ess-bugs-update))
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)
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;;;###autoload
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(define-derived-mode ess-bugs-mode ess-mode "ESS[BUGS]"
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"Major mode for BUGS."
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(setq-local comment-start "#")
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(setq font-lock-defaults '(ess-bugs-font-lock-keywords nil t))
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(setq ess-language "S") ; mimic S for ess-smart-underscore
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(unless (when (fboundp 'w32-shell-dos-semantics)
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(w32-shell-dos-semantics))
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(add-hook 'comint-output-filter-functions 'ess-bugs-exit-notify-sh)))
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;;;###autoload
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(add-to-list 'auto-mode-alist '("\\.[Bb][Uu][Gg]\\'" . ess-bugs-mode))
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;;;###autoload
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(add-to-list 'auto-mode-alist '("\\.[Bb][Oo][Gg]\\'" . ess-bugs-mode))
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;;;###autoload
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(add-to-list 'auto-mode-alist '("\\.[Bb][Mm][Dd]\\'" . ess-bugs-mode))
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(defun ess-sci-to-dec ()
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"For BUGS/S family: Express +/-0.000E+/-0 or +/-0.0e+/-00 as a decimal."
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(interactive)
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(setq buffer-read-only nil)
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(save-excursion (goto-char 0)
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(save-match-data (let ((ess-temp-replacement-string nil)
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(ess-temp-replacement-9 0)
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(ess-temp-replacement-diff 0))
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(while (search-forward-regexp "-?[0-9][.][0-9][0-9]?[0-9]?[Ee][+-][0-9][0-9]?" nil t)
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(setq ess-temp-replacement-string
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(int-to-string (string-to-number (match-string 0))))
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(setq ess-temp-replacement-diff (- (match-end 0) (match-beginning 0)))
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(save-match-data
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(setq ess-temp-replacement-9
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(string-match "99999999999$" ess-temp-replacement-string))
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(if (not ess-temp-replacement-9)
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(setq ess-temp-replacement-9
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(string-match "000000000001$" ess-temp-replacement-string))))
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(if ess-temp-replacement-9
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(setq ess-temp-replacement-string
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(substring ess-temp-replacement-string 0 ess-temp-replacement-9)))
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(setq ess-temp-replacement-diff
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(- ess-temp-replacement-diff (string-width ess-temp-replacement-string)))
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(while (> ess-temp-replacement-diff 0)
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(setq ess-temp-replacement-string (concat ess-temp-replacement-string " "))
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(setq ess-temp-replacement-diff (- ess-temp-replacement-diff 1)))
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(replace-match ess-temp-replacement-string))))))
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(provide 'ess-bugs-d)
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;;; ess-bugs-d.el ends here
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