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- Committer: Bazaar Package Importer
- Author(s): Dirk Eddelbuettel
- Date: 2010-03-03 06:25:04 UTC
- mfrom: (1.2.13 upstream) (3.1.13 sid)
- Revision ID: james.westby@ubuntu.com-20100303062504-rtei3p11s1gmcj4r
Tags: 5.8-1
New upstream version released this morning
- files added:
- lisp/ess-arc-d.el
- files removed:
- lisp/ess-cust.el
- files modified:
- ANNOUNCE
added
removed
lisp/ess-r-d.el
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;;; ess-r-d.el --- R customization
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;; Copyright (C) 1997--2007 A.J. Rossini, Rich M. Heiberger, Martin
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;; Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
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;; Original Author: A.J. Rossini
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;; Created: 12 Jun 1997
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;; Maintainers: ESS-core <ESS-core@stat.math.ethz.ch>
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;; Keywords: start up, configuration.
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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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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to
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;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
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;;; Commentary:
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;;; This file defines all the R customizations for ESS. See ess-s-l.el
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;;; for general S language customizations.
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;;; Autoloads and Requires
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(ess-message "[ess-r-d:] (require 'ess-s-l)")
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(require 'ess-s-l)
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(require 'ess-r-args); for now
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;; modify S Syntax table:
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(setq R-syntax-table S-syntax-table)
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;; In R 2.x, back tick now is a quote character, so lets tell Emacs
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;; that it is; the problem below for older R should no longer be a
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;; serious issue.
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;;R >= 1.8: back tick `string` -- unfortunately no *pair* checking:
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;; breaks when things like `..' are used:
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(modify-syntax-entry ?` "\"" R-syntax-table)
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(modify-syntax-entry ?_ "_" R-syntax-table) ; foo_bar is symbol in R >=1.9
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(ess-message "[ess-r-d:] (autoload ..) & (def** ..)")
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(autoload 'inferior-ess "ess-inf" "Run an ESS process.")
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(autoload 'ess-mode "ess-mode" "Edit an ESS process.")
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;;; Code:
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(defvar R-customize-alist
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(append
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'((ess-local-customize-alist . 'R-customize-alist)
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(ess-dialect . "R")
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(ess-suffix . "R")
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(ess-dump-filename-template . (ess-replace-regexp-in-string
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"S$" ess-suffix ; in the one from custom:
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ess-dump-filename-template-proto))
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(ess-mode-syntax-table . R-syntax-table)
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(ess-mode-editing-alist . R-editing-alist)
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(ess-change-sp-regexp . ess-R-change-sp-regexp)
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(ess-help-sec-regex . ess-help-R-sec-regex)
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(ess-help-sec-keys-alist . ess-help-R-sec-keys-alist)
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(ess-loop-timeout . ess-S-loop-timeout);fixme: dialect spec.
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(ess-cmd-delay . ess-R-cmd-delay)
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(ess-function-pattern . ess-R-function-pattern)
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(ess-object-name-db-file . "ess-r-namedb.el" )
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(ess-imenu-mode-function . 'ess-imenu-R)
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(inferior-ess-program . inferior-R-program-name)
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(inferior-ess-objects-command . inferior-R-objects-command)
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(inferior-ess-font-lock-keywords . inferior-ess-R-font-lock-keywords)
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(inferior-ess-search-list-command . "search()\n")
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;;(inferior-ess-help-command . "help(\"%s\", htmlhelp=FALSE)\n")
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(inferior-ess-help-command . inferior-ess-r-help-command)
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(inferior-ess-help-filetype . nil)
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(inferior-ess-exit-command . "q()")
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(inferior-ess-exit-prompt . "Save workspace image? [y/n/c]: ")
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(inferior-ess-primary-prompt . "\\([A-Z][][A-Za-z0-9.]*\\)?> ")
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(inferior-ess-secondary-prompt . "+ ?")
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;;harmful for shell-mode's C-a: -- but "necessary" for ESS-help?
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(inferior-ess-start-file . nil) ;; "~/.ess-R"
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(inferior-ess-start-args . "")
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(ess-STERM . "iESS")
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(ess-editor . R-editor)
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(ess-pager . R-pager)
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)
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S-common-cust-alist)
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"Variables to customize for R -- set up later than emacs initialization.")
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(defvar ess-r-versions '("R-1" "R-2" "R-devel" "R-patched")
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"List of partial strings for versions of R to access within ESS.
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Each string specifies the start of a filename. If a filename
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beginning with one of these strings is found on `exec-path', a M-x
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command for that version of R is made available. For example, if the
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file \"R-1.8.1\" is found and this variable includes the string
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\"R-1\", a function called `M-x R-1.8.1' will be available to run that
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version of R.
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If duplicate versions of the same program are found (which happens if
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the same path is listed on `exec-path' more than once), they are
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ignored by calling `ess-uniq-list'.
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Set this variable to nil to disable searching for other versions of R.
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If you set this variable, you need to restart Emacs (and set this variable
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before ess-site is loaded) for it to take effect.")
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;;;### autoload
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(defun R (&optional start-args)
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"Call 'R', the 'GNU S' system from the R Foundation.
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Optional prefix (C-u) allows to set command line arguments, such as
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--vsize. This should be OS agnostic.
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If you have certain command line arguments that should always be passed
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to R, put them in the variable `inferior-R-args'."
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(interactive "P")
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(setq ess-customize-alist R-customize-alist)
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(ess-write-to-dribble-buffer ;; for debugging only
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(format
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"\n(R): ess-dialect=%s, buf=%s, start-arg=%s\n current-prefix-arg=%s\n"
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ess-dialect (current-buffer) start-args current-prefix-arg))
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(let* ((r-always-arg
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(if (or ess-microsoft-p (eq system-type 'cygwin))
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"--ess "
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"--no-readline "))
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(r-start-args
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(concat r-always-arg
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inferior-R-args " " ; add space just in case
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(if start-args
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(read-string
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(concat "Starting Args [other than `"
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r-always-arg
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"'] ? "))
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nil)))
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)
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;;Micro$ ?: default-process-coding-system ;-breaks UTF locales on Unix:
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(if ess-microsoft-p
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(setq default-process-coding-system '(undecided-dos . undecided-dos)))
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(inferior-ess r-start-args) ;; -> .. (ess-multi ...) -> .. (inferior-ess-mode) ..
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;;-------------------------
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(ess-write-to-dribble-buffer
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(format "(R): inferior-ess-language-start=%s\n"
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inferior-ess-language-start))
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;; can test only now that R is running:
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(if (ess-current-R-at-least '2.5.0)
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(progn
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(if ess-use-R-completion ;; use R's completion mechanism (pkg "rcompgen" or "utils")
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(progn ; nothing to happen here -- is all in ess-complete-object-name
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(ess-write-to-dribble-buffer "resetting completion to 'ess-R-complete-object-name")
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))
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;; problem with ess-help-command
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(let ((my-R-help-cmd
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(if (ess-current-R-at-least '2.10.0)
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"help"
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;; else R version <= 2.9.2
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"function(..., help_type) help(..., htmlhelp= (help_type==\"html\"))")))
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(ess-eval-linewise
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(concat ".help.ESS <- " my-R-help-cmd) nil nil nil 'wait-prompt)
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))
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;; else R version <= 2.4.1
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;; for R <= 2.1.x : define baseenv() :
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(ess-eval-linewise
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"if(!exists(\"baseenv\", mode=\"function\")) baseenv <- function() NULL"
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nil nil nil 'wait-prompt);; solving "lines running together"
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)
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(if inferior-ess-language-start
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(ess-eval-linewise inferior-ess-language-start
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nil nil nil 'wait-prompt))))
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;;;### autoload
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(defun R-mode (&optional proc-name)
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"Major mode for editing R source. See `ess-mode' for more help."
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(interactive)
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(setq ess-customize-alist R-customize-alist)
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;;(setq imenu-generic-expression R-imenu-generic-expression)
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(ess-mode R-customize-alist proc-name)
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(if (fboundp 'ess-add-toolbar) (ess-add-toolbar))
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;; ECB needs seminatic stuff.
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;; (if (featurep 'semantic)
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;; (setq semantic-toplevel-bovine-table r-toplevel-bovine-table))
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(if ess-imenu-use-S
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(progn (require 'ess-menu)
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(ess-imenu-R)))
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;; MM: ^^^^^^^^^^^ should really use ess-imenu-mode-function from the
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;; alist above!
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)
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(fset 'r-mode 'R-mode)
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(defun ess-r-versions-create ()
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"Generate the `M-x R-x.y' functions for starting other versions of R.
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On MS Windows, this works using `ess-rterm-version-paths'; otherwise,
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see `ess-r-versions' for strings that determine which functions are created.
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The result is a list of the new R defuns, if any, that were created. The
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defuns will normally be placed on the menubar and stored as
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`ess-r-versions-created' upon ESS initialisation."
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(if (not ess-r-versions)
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nil ;nothing to return
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;; else, if ess-r-versions is non-nil, let's try to find those R versions.
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;; This works by creating a temp buffer where the template function is
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;; edited so that X.Y is replaced by the version name
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(let ((versions)
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(eval-buf (get-buffer-create "*ess-temp-r-evals*"))
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(r-versions-created)
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(template
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;; This is the template function used for creating M-x R-X.Y.
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(concat
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"(defun R-X.Y (&optional start-args)
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\"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS.
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This function was generated by `ess-r-versions-create'.\"
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(interactive \"P\")
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(let ((use-dialog-box nil);; Win-only: dialog box won't return a directory
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(inferior-R-program-name \""
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(if ess-microsoft-p "Rterm" "R") "-X.Y\"))
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(R start-args)))
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"
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) ))
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(save-excursion
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(set-buffer eval-buf)
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;; clear the buffer.
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(delete-region (point-min) (point-max))
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;; Find which versions of R we want. Remove the pathname, leaving just
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;; the name of the executable.
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(setq versions
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(if ess-microsoft-p ess-rterm-version-paths
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;; ^^^^^^^^^^^^^^^^^^^^^^^ created in
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;; ./ess-site.el at start
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;; else (non-MS):
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(ess-uniq-list
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(mapcar 'file-name-nondirectory
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(apply 'nconc
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(mapcar 'ess-find-exec-completions
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ess-r-versions))))))
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(ess-write-to-dribble-buffer
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(format "(R): ess-r-versions-create making M-x defuns for \n %s\n"
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(mapconcat 'identity versions "\n ")))
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(if (not ess-microsoft-p)
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(setq r-versions-created versions)) ;keep copy for returning at end.
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;; Iterate over each string in VERSIONS, creating a new defun each time.
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(while versions
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(let* ((version (car versions))
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(this-version version)
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(beg (point)))
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(setq versions (cdr versions))
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(when ess-microsoft-p
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(setq
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version (file-name-nondirectory ;; two levels up; don't want "bin" ...
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(directory-file-name (file-name-directory
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(directory-file-name (file-name-directory version)))))
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r-versions-created (cons version r-versions-created)))
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(insert template)
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(goto-char beg)
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(while (search-forward "R-X.Y" nil t)
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(replace-match version t t))
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(when ess-microsoft-p
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(goto-char beg)
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(while (search-forward "Rterm-X.Y" nil t)
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(replace-match this-version t t)))
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(goto-char (point-max)))
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)
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;; buffer has now been created with defuns, so eval them!
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(eval-buffer)
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(kill-buffer eval-buf)
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)
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r-versions-created)))
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(defvar ess-newest-R nil
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"Stores the newest version of R that has been found. Used as a cache,
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within ess-find-newest-R. Do not use this value directly, but
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instead call the function \\[ess-find-newest-R].")
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(defun ess-find-newest-R ()
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"Find the newest version of R on the system. Once the value is found,
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cache it in the variable `ess-newest-R' for future use as finding the
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newest version of R can be potentially time-consuming."
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(or ess-newest-R
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(progn (message "Finding all versions of R on your system...")
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;;(sleep-for 3)
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nil)
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(setq ess-newest-R
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(ess-newest-r
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(if ess-microsoft-p
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ess-rterm-version-paths
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(add-to-list 'ess-r-versions-created
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inferior-R-program-name))))))
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(defun ess-check-R-program-name ()
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"Check if `inferior-R-program-name' points to an executable version of R.
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If not, try to find the newest version of R elsewhere on the system, and
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update `inferior-R-program-name' accordingly."
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(unless (executable-find inferior-R-program-name)
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;; need to check if we can find another name.
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(let ((newest (ess-find-newest-R)))
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(if newest
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(setq inferior-R-program-name newest)
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(message "Sorry, no version of R could be found on your system.")))))
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(defun R-newest (&optional start-args)
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"Find the newest version of R available, and run it.
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Subsequent calls to R-newest will run that version, rather than searching
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again for the newest version. Providing an optional prefix arg (C-u) will
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prompt for command line arguments."
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(interactive "P")
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(let ((rnewest (ess-find-newest-R)))
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(if (not rnewest)
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(error "No version of R could be found.")
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;; Else: we have a working version of R.
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;; Have to be careful to avoid recursion...
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(message (concat "Newest version of R is " rnewest))
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(fset 'R-newest
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(intern
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(if ess-microsoft-p
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(file-name-nondirectory
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(substring (file-name-directory
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(substring (file-name-directory rnewest) 0 -1))
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0 -1))
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rnewest)))
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;;(fset 'R-newest (intern rnewest))
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(R-newest start-args))))
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;; (ess-r-version-date "R-2.5.1") (ess-r-version-date "R-patched")
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;; (ess-r-version-date "R-1.2.1") (ess-r-version-date "R-1.8.1")
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;; Note that for R-devel, ver-string is something like
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;; R version 2.6.0 Under development (unstable) (2007-07-14 r42234)
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;; Antique examples are 'R 1.0.1 (April 14, 2000)' or 'R 1.5.1 (2002-06-17).'
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(defun ess-r-version-date (rver)
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"Return the date of the version of R named RVER.
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The date is returned as a date string. If the version of R could
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not be found from the output of the RVER program, \"-1\" is
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returned."
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(let (ver-string
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(date "-1"))
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(setq ver-string (shell-command-to-string
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(concat rver " --version")))
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(when (string-match
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"R \\(version \\)?[1-9][^\n]+ (\\(2[0-9-]+\\)\\( r[0-9]+\\)?)"
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ver-string)
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(setq date (match-string 2 ver-string)))
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(cons date rver)))
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(defun ess-current-R-version ()
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"Get the version of R currently running in the ESS buffer as a string"
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(ess-make-buffer-current)
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(car (ess-get-words-from-vector "as.character(getRversion())\n")))
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(defun ess-current-R-at-least (version)
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"Is the version of R (in the ESS buffer) at least (\">=\") VERSION ?
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Examples: (ess-current-R-at-least '2.7.0)
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or (ess-current-R-at-least \"2.5.1\")"
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(ess-make-buffer-current)
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(string= "TRUE"
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(car (ess-get-words-from-vector
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(format "as.character(getRversion() >= \"%s\")\n" version)))))
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(defun ess-newest-r (rvers)
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"Check all the versions of RVERS to see which is the newest.
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Return the name of the newest version of R."
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(let ((rtimes (mapcar 'ess-r-version-date rvers)))
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;; SJE: 2007-07-13 -- following line is a temp var to check that
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;; the newest version of R is found correctly.
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(setq ess-temp-newest rtimes)
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(ess-find-newest-date rtimes)))
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;; Test case for following defun:
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;; (setq a '( ("2003-10-04" . "R-1.7")
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;; ("2006-11-19" . "R-2.2")
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;; ("2007-07-01" . "R-dev")
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;; ("-1" . "R-broken")
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;; ("2005-12-30" . "R-2.0")))
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;; (ess-find-newest-date a)
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(defun ess-find-newest-date (rvers)
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"Find the newest version of R given in the a-list RVERS.
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Each element of RVERS is a dotted pair (date . R-version), where
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date is given as e.g.\"2007-11-30\" so that we can compare dates
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as strings. If a date is listed as \"-1\", that version of R
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could not be found.
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If the value returned is nil, no valid newest version of R could be found."
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(let (new-r this-r
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(new-time "0"))
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(while rvers
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(setq this-r (car rvers)
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rvers (cdr rvers))
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(when (string< new-time (car this-r))
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(setq new-time (car this-r)
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new-r (cdr this-r))))
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new-r))
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(defun ess-find-rterm (&optional ess-R-root-dir)
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"Find the full path of all occurences of Rterm.exe under the ESS-R-ROOT-DIR.
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If ESS-R-ROOT-DIR is nil, construct it by looking for an occurence of Rterm.exe
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in the exec-path. If there are no occurences of Rterm.exe in the exec-path,
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then use `ess-program-files' (which evaluates to something like \"c:/progra~1/R/\"
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in English locales) which is the default location for the R distribution."
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(if (not ess-R-root-dir)
411
(let ((Rpath (executable-find "Rterm")))
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(setq ess-R-root-dir
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(expand-file-name
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(if Rpath
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(concat (file-name-directory Rpath) "../../")
416
(concat ess-program-files "/R/"))))
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(ess-write-to-dribble-buffer
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(format "(ess-find-rterm): ess-R-root-dir = '%s'\n" ess-R-root-dir))
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))
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(when (file-directory-p ess-R-root-dir) ; otherwise file-name-all-.. errors
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(setq ess-R-root-dir
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(ess-replace-regexp-in-string "[\\]" "/" ess-R-root-dir))
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(let ((R-ver
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(ess-drop-non-directories
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(ess-flatten-list
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(mapcar '(lambda (r-prefix)
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(file-name-all-completions r-prefix ess-R-root-dir))
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(append '("rw") ess-r-versions))))))
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(mapcar '(lambda (dir)
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(concat ess-R-root-dir
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(ess-replace-regexp-in-string "[\\]" "/" dir)
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"bin/Rterm.exe"))
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R-ver))))
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;; From Jim (James W.) MacDonald, based on code by Deepayan Sarkar,
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;; originally named 'alt-ess-complete-object-name'.
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;; Use rcompgen in ESS
439
;; Can be activated by something like
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;; (define-key inferior-ess-mode-map "\t" 'ess-R-complete-object-name)
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(defun ess-R-complete-object-name ()
442
"Completion in R via R's completion utilities (formerly 'rcompgen').
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To be used instead of ESS' completion engine for R versions >= 2.5.0
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(or slightly older versions of R with an attached and working 'rcompgen' package)."
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(interactive)
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(ess-make-buffer-current)
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(let* ((comint-completion-addsuffix nil)
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(beg-of-line (save-excursion (comint-bol nil) (point)))
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(end-of-line (point-at-eol))
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(line-buffer (buffer-substring beg-of-line end-of-line))
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(NS (if (ess-current-R-at-least '2.7.0)
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"utils:::"
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"rcompgen:::"))
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(token-string ;; setup, including computation of the token
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(progn
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(ess-command
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(format (concat NS ".assignLinebuffer('%s')\n") line-buffer))
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(ess-command (format (concat NS ".assignEnd(%d)\n")
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(- (point) beg-of-line)))
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(car (ess-get-words-from-vector
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(concat NS ".guessTokenFromLine()\n")))))
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(possible-completions ;; compute and retrieve possible completions
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(progn
465
(ess-command (concat NS ".completeToken()\n"))
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(ess-get-words-from-vector
467
(concat NS ".retrieveCompletions()\n")))))
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(or (comint-dynamic-simple-complete token-string
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possible-completions)
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'none)))
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;;;### autoload
474
(defun Rnw-mode ()
475
"Major mode for editing Sweave(R) source.
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See `noweb-mode' and `R-mode' for more help."
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(interactive)
478
(require 'ess-noweb);; << probably someplace else
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(noweb-mode 1); turn it on
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(noweb-set-doc-mode 'latex-mode)
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(noweb-set-code-mode 'R-mode)
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(run-hooks 'Rnw-mode-hook))
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(fset 'Snw-mode 'Rnw-mode); just a synonym (for now or ever)
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(autoload 'ess-transcript-mode "ess-trns"
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"Major mode for editing S transcript files." t)
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(defun R-transcript-mode ()
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"Does the right thing."
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(interactive)
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(ess-transcript-mode R-customize-alist))
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(fset 'r-transcript-mode 'R-transcript-mode)
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(defun R-fix-T-F (&optional from quietly)
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"Fix T/F into TRUE and FALSE *cautiously*, i.e. not in comments and strings;
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starting from the current position (point)."
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(interactive "d\nP"); point and prefix (C-u)
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(save-excursion
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(goto-char from)
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(ess-rep-regexp "\\(\\([][=,()]\\|<-\\) *\\)T\\>" "\\1TRUE"
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'fixcase nil (not quietly))
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(goto-char from)
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(ess-rep-regexp "\\(\\([][=,()]\\|<-\\) *\\)F\\>" "\\1FALSE"
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'fixcase nil (not quietly))))
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;; From: Sebastian Luque <spluque@gmail.com>
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;; To: ess-help@stat.math.ethz.ch
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;; Date: Mon, 01 May 2006 19:17:49 -0500
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;; Without knowing how to tell R to use w3m from within Emacs, and after
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;; switching to Konqueror's window for the millionth time, I wrote the
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;; following function:
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;; This emulates some of the functionality of RSiteSearch() and tests ok in
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;; my system GNU Emacs 22.0.50.1 (i486-pc-linux-gnu, X toolkit, Xaw3d scroll
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;; bars) of 2006-04-27 on pacem, modified by Debian. This has the benefit of
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;; displaying results with whatever you've told browse-url to use; in my
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;; case, w3m with the emacs-w3m package.
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;; My elisp skills are rather poor, so comments and suggestions for
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;; improvement are welcome.
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;; --
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;; Seb
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;; MM _FIXME_: This only works correctly for Emacs 22.0.50 (alpha)
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;; for 21.x it has problems in the (completing-read-multiple .)
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;; at the end
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(defun R-site-search (string)
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"Search the R archives for STRING, using default criteria. If
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called with a prefix, options are available for
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1) matches per page,
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2) sections of the archives to search (separated by value of `crm-default-separator'),
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3) for displaying results in long or short formats, and
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4) for sorting by any given field.
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Completion is available for supplying options."
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(interactive "sSearch string: ")
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(let ((site "http://search.r-project.org/cgi-bin/namazu.cgi?query=")
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(okstring (replace-regexp-in-string " +" "+" string)))
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(if current-prefix-arg
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(let ((mpp (concat
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"&max="
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(completing-read
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"Matches per page: "
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'(("20" 1) ("30" 2) ("40" 3) ("50" 4) ("100" 5)))))
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(format (concat
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"&result="
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(completing-read
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"Format: " '("normal" "short")
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nil t "normal" nil "normal")))
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(sortby (concat
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"&sort="
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(completing-read
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"Sort by: "
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'(("score" 1) ("date:late" 2) ("date:early" 3)
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("field:subject:ascending" 4)
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("field:subject:decending" 5)
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("field:from:ascending" 6) ("field:from:decending" 7)
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("field:size:ascending" 8) ("field:size:decending" 9))
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nil t "score" nil "score")))
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(restrict (concat
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"&idxname="
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(mapconcat
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'identity
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(completing-read-multiple
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"Limit search to: "
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'(("Rhelp02a" 1) ("functions" 2) ("docs" 3)
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("Rhelp01" 4))
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nil t "Rhelp02a,functions,docs" nil
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"Rhelp02a,functions,docs") "&idxname="))))
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(browse-url (concat site okstring mpp format sortby restrict)))
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;; else: without prefix use defaults:
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(browse-url (concat site okstring "&max=20&result=normal&sort=score"
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"&idxname=Rhelp02a&idxname=functions&idxname=docs")))))
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; provides
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(provide 'ess-r-d)
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; Local variables section
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;;; This file is automatically placed in Outline minor mode.
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;;; The file is structured as follows:
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;;; Chapters: ^L ;
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;;; Sections: ;;*;;
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;;; Subsections: ;;;*;;;
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;;; Components: defuns, defvars, defconsts
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;;; Random code beginning with a ;;;;* comment
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;;; Local variables:
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;;; mode: emacs-lisp
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;;; outline-minor-mode: nil
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;;; mode: outline-minor
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;;; outline-regexp: "\^L\\|\\`;\\|;;\\*\\|;;;\\*\\|(def[cvu]\\|(setq\\|;;;;\\*"
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;;; End:
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;;; ess-r-d.el ends here
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