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491 lines
18 KiB
491 lines
18 KiB
;;; ess-swv.el --- Some simple functions for ESS and Sweave
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;; Copyright (C) 2005 David Whiting, A.J. Rossini, Richard M. Heiberger, Martin
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;; Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
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;; Copyright (C) 2006-2008 A.J. Rossini, Richard M. Heiberger, Martin Maechler,
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;; Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
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;; Author: David Whiting <david.whiting@ncl.ac.uk>
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;; Created: 15 April 2005
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;; Maintainer: ESS-core <ESS-core@r-project.org>
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;; Keywords: statistics, tools
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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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;; 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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;; 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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;;; Commentary:
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;;
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;; Some simple functions for ESS and Sweave
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;; david.whiting at ncl.ac.uk
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;; Wed Sep 1 14:55:52 CEST 2004
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;; I have written some very simple elisp functions that I have found
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;; useful and thought others might like to see. I dabble with elisp
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;; occasionally at best so there are probably better ways to do what I
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;; have done, but so far this seems to work for me. There are several
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;; things that are hard-coded, I use Linux and I think that this would
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;; probably not work in Windows (not as it is now anyway).
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;; With these functions and key bindings all I need to do is open a .Rnw
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;; file and, assuming R is running, I press:
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;; M-n s to Sweave the file, then
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;; M-n l to run latex on the results of Sweave, then
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;; M-n p to make and display a postscript file , or
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;; M-n P to make and display a PDF version.
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;; David Whiting to Anthony Rossini, Mar 30
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;; On Wed, Mar 30, 2005 at 11:51:26AM +0200, A.J. Rossini wrote:
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;; > I'm going to go ahead and add this stuff to the distribution tonight
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;; > if you don't mind. I'd forgotten about it!
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;; It would make me very happy indeed.
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;; > (however, need permission to do so).
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;; Permission granted!
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;; Dave
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;; --
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;; David Whiting
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;; School of Clinical Medical Sciences, The Medical School
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;; University of Newcastle upon Tyne, NE2 4HH, UK.
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;;; TODO:
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;;;
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;;; 1. I want to be able to send ess-swv-latex a parameter to tell it
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;;; the number of times to run LaTeX (to get references updated
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;;; correctly).
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;;;
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;;; 2. Also need to add ess-swv-Bibtex.
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;;;
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;;; 3. Might be good to have a way to chain commands.
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;;;
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;;; 4. ADD to the ../doc/ess.texi !!
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;;; Code:
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;;; Autoloads and Requires
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(eval-when-compile
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(require 'ess-custom))
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(require 'ess-utils)
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(require 'ess-noweb-mode)
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(require 'ess-r-mode); for Rnw-mode
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(require 'easymenu)
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(defvar TeX-command-list)
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(defvar TeX-command-default)
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(defvar TeX-file-extensions)
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(declare-function TeX-normal-mode "tex")
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(defgroup ess-sweave nil
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"Mode for editing Sweave (*.[SR]nw) files."
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:group 'ess-S
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:prefix "ess-")
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(defcustom ess-pdf-viewer-pref nil
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"External pdf viewer you like to use from ESS.
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Can be a string giving a name of the program or a list with car
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giving heprogram and the tail giving the arguments. For example
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'(\"okular\" \"--unique\")."
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:type '(choice (const nil) (repeat :tag "Command with arguments" string) (string :tag "Command")))
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(defcustom ess-ps-viewer-pref nil
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"External PostScript viewer you like to use from ESS.
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If nil, ESS will try finding one from a list."
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:type '(choice (const nil) string))
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(defcustom ess-swv-pdflatex-commands '("texi2pdf" "pdflatex" "make")
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"Commands to run a version of pdflatex in \\[ess-swv-PDF];
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the first entry is the default command."
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:group 'ess-sweave
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:type '(repeat string))
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(defcustom ess-swv-plug-into-AUCTeX-p nil
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"Non-nil means add commands to AUCTeX's \\[TeX-command-list]
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to sweave the current noweb file and latex the result."
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:group 'ess-sweave
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:type '(choice (const :tag "Off" nil)
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(const :tag "On" t)))
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(defcustom ess-swv-processing-command ".ess_weave(%s, %s)"
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"Command used by `ess-swv-run-in-R'.
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First %s is literally replaced by the processing command (for
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example: Sweave) second %s is replaced with a string containing a
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processed file and possibly additional argument encoding (example:
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\"path/to/foo.Rnw\", encoding='utf-8')
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.ess_weave changes the working directory to that of the supplied
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file.
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If you want to simply call knitr or Sweave in global environment
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set this command to \"%s(%s)\"."
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:group 'ess-R
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:type 'string)
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;; currently use exactly for "Sweave", "Stangle", "knit", and "purl"
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(defun ess-swv-run-in-R (cmd &optional choose-process block)
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"Run \\[cmd] on the current .Rnw file. Utility function not called by user."
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(let* ((rnw-buf (current-buffer)))
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(if choose-process ;; previous behavior
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(ess-force-buffer-current "R process to load into: ")
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;; else
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(update-ess-process-name-list)
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(cond ((= 0 (length ess-process-name-list))
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(message "no ESS processes running; starting R")
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(sit-for 1); so the user notices before the next msgs/prompt
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(run-ess-r)
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(set-buffer rnw-buf)
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)
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((not (string= "R" (ess-make-buffer-current))); e.g. Splus, need R
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(ess-force-buffer-current "R process to load into: "))
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))
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(save-excursion
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;; (ess-execute (format "require(tools)")) ;; Make sure tools is loaded.
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(basic-save-buffer); do not Sweave/Stangle old version of file !
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(let* ((sprocess (ess-get-process ess-current-process-name))
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(sbuffer (process-buffer sprocess))
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(rnw-file (buffer-file-name))
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(Rnw-dir (file-name-directory rnw-file))
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(buf-coding (symbol-name buffer-file-coding-system))
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;; could consider other encodings, but utf-8 is "R standard" for non-ASCII:
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(cmd-args (concat "\"" rnw-file "\""
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(if (string-match "^utf-8" buf-coding)
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", encoding = \"utf-8\"")))
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(Sw-cmd
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(format ess-swv-processing-command cmd cmd-args)))
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(message "%s()ing %S" cmd rnw-file)
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;; need to block when we are running ess-swv-weave-PDF so we
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;; know when to start compiling the generated .tex file
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(if block
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(progn
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(ess-eval-linewise (concat Sw-cmd "\n") nil nil nil t)
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(message "Finished %s()ing %S" cmd rnw-file))
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(ess-execute Sw-cmd 'buffer nil nil)
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(pop-to-buffer-same-window rnw-buf)
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(display-buffer (buffer-name sbuffer)))))))
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(defcustom ess-swv-processor 'sweave
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"Processor to use for weaving and tangling.
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Currently 'sweave or 'knitr"
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:group 'ess-R
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:type '(choice (const sweave) (const knitr)))
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(defun ess-swv-tangle ()
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"Run Stangle/purl on the current .Rnw file.
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Depending on the `ess-swv-processor' used."
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(interactive)
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(ess-swv-run-in-R (cond ((eq ess-swv-processor 'sweave) "Stangle")
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((eq ess-swv-processor 'knitr) "purl")
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(t (error "Not a valid processor %s" ess-swv-processor)))))
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(defun ess-swv-weave (&optional choose)
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"Run Sweave/knit on the current .Rnw file.
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Depending on the `ess-swv-processor' used.
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If CHOOSE is non-nil, offer a menu of available weavers.
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"
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(interactive "P")
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(let ((processor (if choose
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(ess-completing-read "Weaver" '("sweave" "knitr") nil t)
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(symbol-name ess-swv-processor))))
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(ess-swv-run-in-R (cond ((string= processor "sweave") "Sweave")
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((string= processor "knitr") "knit")
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(t (error "Not a valid processor %s" processor))))))
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(defun ess-swv-sweave ()
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"Run Sweave on the current .Rnw file."
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(interactive)
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(ess-swv-run-in-R "Sweave"))
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(defun ess-swv-stangle ()
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"Run Stangle on the current .Rnw file."
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(interactive)
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(ess-swv-run-in-R "Stangle"))
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(defun ess-swv-knit ()
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"Run knit on the current .Rnw file."
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(interactive)
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(ess-swv-run-in-R "knit"))
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(defun ess-swv-purl ()
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"Run purl on the current .Rnw file."
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(interactive)
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(ess-swv-run-in-R "purl"))
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;; trying different viewers; thanks to an original patch for
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;; ess-swv.el from Leo <sdl@web.de> :
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(defun ess-get-ps-viewer ()
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"Get external PostScript viewer to be used from ESS.
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Use `ess-ps-viewer-pref' when that is executably found by \\[executable-find].
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Otherwise try a list of fixed known viewers."
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(file-name-nondirectory
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(or (and ess-ps-viewer-pref ; -> ./ess-custom.el
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(executable-find ess-ps-viewer-pref))
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(executable-find "gv")
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(executable-find "evince")
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(executable-find "kghostview"))))
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(defun ess-get-pdf-viewer ()
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"Get external PDF viewer to be used from ESS.
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Use `ess-pdf-viewer-pref' when that is executably found by \\[executable-find].
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Otherwise try a list of fixed known viewers."
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(let ((viewer (or ess-pdf-viewer-pref
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;; (and (stringp ess-pdf-viewer-pref) ; -> ./ess-custom.el
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;; (executable-find ess-pdf-viewer-pref))
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(executable-find "evince")
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(executable-find "kpdf")
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(executable-find "okular")
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(executable-find "xpdf")
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(executable-find "acroread")
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(executable-find "xdg-open")
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;; this one is wrong, (ok for time being as it is used only in swv)
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(when (fboundp 'ess-get-words-from-vector)
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(car (ess-get-words-from-vector
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"getOption(\"pdfviewer\")\n"))))))
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(when (stringp viewer)
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(setq viewer (file-name-nondirectory viewer)))
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viewer))
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(defun ess-swv-weave-PDF (&optional choose)
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"Sweave/knit, compile TeX, and display PDF.
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Run Sweave or knit depending on `ess-swv-processor' used.
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If CHOOSE is non-nil, offer a menu of available weavers.
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"
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(interactive "P")
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(let ((processor (if choose
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(ess-completing-read "Weaver" '("sweave" "knitr") nil t)
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(symbol-name ess-swv-processor))))
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(ess-swv-run-in-R (cond ((string= processor "sweave") "Sweave")
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((string= processor "knitr") "knit")
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(t (error "Not a valid processor %s" processor)))
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nil t)
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(ess-swv-PDF nil t)))
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(defun ess-swv-latex ()
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"Run LaTeX on the product of Sweave()ing the current file."
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(interactive)
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(save-excursion
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(let* ((namestem (file-name-sans-extension (buffer-file-name)))
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(latex-filename (concat namestem ".tex"))
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(tex-buf (get-buffer-create " *ESS-tex-output*")))
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(message "Running LaTeX on '%s' ..." latex-filename)
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(switch-to-buffer tex-buf)
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(call-process "latex" nil tex-buf 1 latex-filename)
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(switch-to-buffer (buffer-name))
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(display-buffer tex-buf)
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(message "Finished running LaTeX" ))))
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(defun ess-swv-PS ()
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"Create a postscript file from a dvi file (name based on the current
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Sweave file buffer name) and display it."
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(interactive)
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(let* ((buf (buffer-name))
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(namestem (file-name-sans-extension (buffer-file-name)))
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(dvi-filename (concat namestem ".dvi"))
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(psviewer (ess-get-ps-viewer)))
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(shell-command (concat "dvips -o temp.ps " dvi-filename))
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(shell-command (concat psviewer " temp.ps & "))
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(switch-to-buffer buf)
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))
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(defun ess-swv-PDF (&optional pdflatex-cmd hide-compile-buffer)
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"From LaTeX file, create a PDF (via 'texi2pdf' or 'pdflatex', ...), by
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default using the first entry of `ess-swv-pdflatex-commands' and display it."
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(interactive)
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(setq pdflatex-cmd
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(or pdflatex-cmd
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(and (eq (length ess-swv-pdflatex-commands) 1)
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(car ess-swv-pdflatex-commands))
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(ess-completing-read "pdf latex command"
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ess-swv-pdflatex-commands ; <- collection to choose from
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nil 'confirm ; or 'confirm-after-completion
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nil nil (car ess-swv-pdflatex-commands))))
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(let* ((buf (buffer-name))
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(namestem (file-name-sans-extension (buffer-file-name)))
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(latex-filename (concat namestem ".tex"))
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(tex-buf (get-buffer-create "*ESS-tex-output*"))
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(pdfviewer (ess-get-pdf-viewer))
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(pdf-status)
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(cmdstr-win (format "start \"%s\" \"%s.pdf\"" pdfviewer namestem))
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(pdffile (format "%s.pdf" namestem))
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(cmd (if (stringp pdfviewer)
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(list pdfviewer pdffile)
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(append pdfviewer (list pdffile)))))
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;;(shell-command (concat "pdflatex " latex-filename))
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(message "Running '%s' on '%s' ..." pdflatex-cmd latex-filename)
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(with-current-buffer tex-buf (erase-buffer))
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(setq pdf-status
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(call-process pdflatex-cmd nil tex-buf t
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(if (string= "texi2" (substring pdflatex-cmd 0 5))
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;; workaround (bug?): texi2pdf or texi2dvi *fail* to work with full path:
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(file-name-nondirectory latex-filename)
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latex-filename)))
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(if (not (= 0 pdf-status))
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(progn (message "** OOPS: error in '%s' (%d)!" pdflatex-cmd pdf-status)
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(display-buffer tex-buf))
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;; else: pdflatex probably ok
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;; (set-process-sentinel proc 'shell-command-sentinel)
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(if (and (and ess-microsoft-p
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;; Silence byte compiler warns about w32-fns
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(fboundp 'w32-shell-dos-semantics))
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(w32-shell-dos-semantics))
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(shell-command cmdstr-win)
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(message "%s" (mapconcat 'identity cmd " "))
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(apply 'start-process (car cmd) nil cmd))
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(unless hide-compile-buffer (display-buffer tex-buf))
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(message "%s finished with status %d" pdflatex-cmd pdf-status))))
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(defun ess-insert-Sexpr ()
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"Insert Sexpr{} into the buffer at point."
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(interactive)
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(insert "\\Sexpr{}")
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(backward-char))
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;;; back-compatible wrappers:
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(defun ess-makeSweave () "old *DEPRECATED* version of \\[ess-swv-weave]."
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(interactive) (ding)
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(message
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"** warning: ess-makeSweave is deprecated. Do use (ess-swv-weave) instead!")
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(ess-swv-weave))
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(defun ess-makeLatex () "old *DEPRECATED* version of \\[ess-swv-latex]."
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(interactive) (ding)
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(message
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"** warning: ess-makeLatex is deprecated. Do use (ess-swv-latex) instead!")
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(ess-swv-latex))
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(defun ess-makePS () "old *DEPRECATED* version of \\[ess-swv-PS]."
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(interactive) (ding)
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(message
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"** warning: ess-makePS is deprecated. Do use (ess-swv-PS) instead!")
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(ess-swv-PS))
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(defun ess-makePDF () "old *DEPRECATED* version of \\[ess-swv-PDF]."
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(interactive) (ding)
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(message
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"** warning: ess-makePDF is deprecated. Do use (ess-swv-PDF) instead!")
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(ess-swv-PDF))
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;; AUCTeX integration. This is independent of this library, but it fits
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;; here nonetheless since it's an alternative way of Sweave'ing without
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;; starting iESS.
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(defun ess-swv-add-TeX-commands ()
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"Add commands to AUCTeX's \\[TeX-command-list]."
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(unless (and (featurep 'tex-site) (featurep 'tex))
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(error "AUCTeX does not seem to be loaded"))
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(add-to-list 'TeX-command-list
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'("Sweave" "R CMD Sweave %t"
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TeX-run-command nil (latex-mode) :help
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"Run Sweave") t)
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(add-to-list 'TeX-command-list
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'("LaTeXSweave" "%l %(mode) %s"
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TeX-run-TeX nil (latex-mode) :help
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"Run LaTeX after Sweave") t)
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(setq TeX-command-default "Sweave")
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(mapc (lambda (suffix)
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(add-to-list 'TeX-file-extensions suffix))
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'("nw" "Snw" "Rnw")))
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(defun ess-swv-remove-TeX-commands (x)
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"Helper function: check if car of X is one of the Sweave strings"
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(let ((swv-cmds '("Sweave" "LaTeXSweave")))
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(unless (member (car x) swv-cmds) x)))
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(defun ess-swv-plug-into-AUCTeX ()
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"Add commands to AUCTeX's \\[TeX-command-list] to sweave the current noweb
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file and latex the result."
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(if ess-swv-plug-into-AUCTeX-p
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(add-hook 'Rnw-mode-hook 'ess-swv-add-TeX-commands)
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(remove-hook 'Rnw-mode-hook 'ess-swv-add-TeX-commands)
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(setq TeX-command-list (mapcar 'ess-swv-remove-TeX-commands TeX-command-list)
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;; this will remove the items, leaving nils, so remove them.
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TeX-command-list (delq nil TeX-command-list))))
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;; as ess-swv-plug-into-AUCTeX-p is customizable ... :
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(if ess-swv-plug-into-AUCTeX-p
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(eval-after-load "tex" '(ess-swv-plug-into-AUCTeX)))
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(defun ess-swv-toggle-plug-into-AUCTeX ()
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"Toggle inclusion of commands to sweave noweb files and latex the results in
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\\[TeX-command-list] on and off. Commands are added via \\[Rnw-mode-hook]."
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(interactive)
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(unless (and (featurep 'tex-site) (featurep 'tex))
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(error "AUCTeX are not available"))
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(setq ess-swv-plug-into-AUCTeX-p (not ess-swv-plug-into-AUCTeX-p))
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(ess-swv-plug-into-AUCTeX)
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(TeX-normal-mode t)
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(if ess-swv-plug-into-AUCTeX-p
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(message "Sweave and LaTeXSweave are activated in AUCTeX.")
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(message "Sweave and LaTeXSweave are de-activated in AUCTeX.")))
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;;; Now bind some keys.
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(define-key ess-noweb-minor-mode-map "\M-ns" 'ess-swv-sweave)
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(define-key ess-noweb-minor-mode-map "\M-nT" 'ess-swv-tangle)
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(define-key ess-noweb-minor-mode-map "\M-nl" 'ess-swv-latex)
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(define-key ess-noweb-minor-mode-map "\M-np" 'ess-swv-PS)
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(define-key ess-noweb-minor-mode-map "\M-nP" 'ess-swv-PDF)
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(define-key ess-noweb-minor-mode-map "\M-nr" 'ess-swv-knit)
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(define-key ess-noweb-minor-mode-map "\M-nu" 'ess-swv-purl)
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(define-key ess-noweb-minor-mode-map "\M-nv" 'ess-swv-weave-PDF)
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(define-key ess-noweb-minor-mode-map "\M-nw" 'ess-swv-weave); depends on proc.
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(define-key ess-noweb-minor-mode-map "\M-nx" 'ess-insert-Sexpr)
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;; AND add these to the noweb menu we have anyway ! :
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(easy-menu-define ess-swv-menu
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ess-noweb-minor-mode-menu
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"Submenu for use in `Rnw-mode'."
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'("Sweaving, Tangling, ..."
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["Sweave" ess-swv-sweave t]
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["Tangle" ess-swv-tangle t]
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["LaTeX" ess-swv-latex t]
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["PDF(LaTeX)" ess-swv-PDF t]
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["PS (dvips)" ess-swv-PS t]
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["Knit" ess-swv-knit t]
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["Purl" ess-swv-purl t]
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["View PDF" ess-swv-weave-PDF t]
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["Weave (Sweave/Knit)" ess-swv-weave t]
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["Insert Sexpr" ess-insert-Sexpr t]
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["AUCTeX Interface" ess-swv-toggle-plug-into-AUCTeX
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:style toggle :selected ess-swv-plug-into-AUCTeX-p]
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))
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(easy-menu-add-item ess-noweb-minor-mode-menu
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nil ;; <= path
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ess-swv-menu)
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; provides
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(provide 'ess-swv)
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;;; ess-swv.el ends here
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