;;; essd-r.el --- R customization ;; Copyright (C) 1997--2007 A.J. Rossini, Rich M. Heiberger, Martin ;; Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen. ;; Original Author: A.J. Rossini ;; Created: 12 Jun 1997 ;; Maintainers: ESS-core ;; Keywords: start up, configuration. ;; This file is part of ESS. ;; This file is free software; you can redistribute it and/or modify ;; it under the terms of the GNU General Public License as published by ;; the Free Software Foundation; either version 2, or (at your option) ;; any later version. ;; This file is distributed in the hope that it will be useful, ;; but WITHOUT ANY WARRANTY; without even the implied warranty of ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;; GNU General Public License for more details. ;; You should have received a copy of the GNU General Public License ;; along with GNU Emacs; see the file COPYING. If not, write to ;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA. ;;; Commentary: ;;; This file defines all the R customizations for ESS. See essl-s.el ;;; for general S language customizations. ;;; Autoloads and Requires (ess-message "[essd-r:] (require 'essl-s)") (require 'essl-s) (require 'essd-r-args); for now ;; modify S Syntax table: (setq R-syntax-table S-syntax-table) ;; In R 2.x, back tick now is a quote character, so lets tell Emacs ;; that it is; the problem below for older R should no longer be a ;; serious issue. ;;R >= 1.8: back tick `string` -- unfortunately no *pair* checking: ;; breaks when things like `..' are used: (modify-syntax-entry ?` "\"" R-syntax-table) (modify-syntax-entry ?_ "_" R-syntax-table) ; foo_bar is symbol in R >=1.9 (ess-message "[essd-r:] (autoload ..) & (def** ..)") (autoload 'inferior-ess "ess-inf" "Run an ESS process.") (autoload 'ess-mode "ess-mode" "Edit an ESS process.") ;;; Code: (defvar R-customize-alist (append '((ess-local-customize-alist . 'R-customize-alist) (ess-dialect . "R") (ess-suffix . "R") (ess-dump-filename-template . (ess-replace-regexp-in-string "S$" ess-suffix ; in the one from custom: ess-dump-filename-template-proto)) (ess-mode-syntax-table . R-syntax-table) (ess-mode-editing-alist . R-editing-alist) (ess-change-sp-regexp . ess-R-change-sp-regexp) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . ess-help-R-sec-keys-alist) (ess-loop-timeout . ess-S-loop-timeout);fixme: dialect spec. (ess-cmd-delay . ess-R-cmd-delay) (ess-function-pattern . ess-R-function-pattern) (ess-object-name-db-file . "ess-r-namedb.el" ) (ess-imenu-mode-function . 'ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . inferior-R-objects-command) (inferior-ess-font-lock-keywords . inferior-ess-R-font-lock-keywords) (inferior-ess-search-list-command . "search()\n") ;;(inferior-ess-help-command . "help(\"%s\", htmlhelp=FALSE)\n") (inferior-ess-help-command . inferior-ess-r-help-command) (inferior-ess-help-filetype . nil) (inferior-ess-exit-command . "q()") (inferior-ess-exit-prompt . "Save workspace image? [y/n/c]: ") (inferior-ess-primary-prompt . "\\([A-Z][][A-Za-z0-9.]*\\)?> ") (inferior-ess-secondary-prompt . "+ ?") ;;harmful for shell-mode's C-a: -- but "necessary" for ESS-help? (inferior-ess-start-file . nil) ;; "~/.ess-R" (inferior-ess-start-args . "") (ess-STERM . "iESS") (ess-editor . R-editor) (ess-pager . R-pager) ) S-common-cust-alist) "Variables to customize for R -- set up later than emacs initialization.") (defvar ess-r-versions '("R-1" "R-2" "R-devel" "R-patched") "List of partial strings for versions of R to access within ESS. Each string specifies the start of a filename. If a filename beginning with one of these strings is found on `exec-path', a M-x command for that version of R is made available. For example, if the file \"R-1.8.1\" is found and this variable includes the string \"R-1\", a function called `M-x R-1.8.1' will be available to run that version of R. If duplicate versions of the same program are found (which happens if the same path is listed on `exec-path' more than once), they are ignored by calling `ess-uniq-list'. Set this variable to nil to disable searching for other versions of R. If you set this variable, you need to restart Emacs (and set this variable before ess-site is loaded) for it to take effect.") ;;;### autoload (defun R (&optional start-args) "Call 'R', the 'GNU S' system from the R Foundation. Optional prefix (C-u) allows to set command line arguments, such as --vsize. This should be OS agnostic. If you have certain command line arguments that should always be passed to R, put them in the variable `inferior-R-args'." (interactive "P") (setq ess-customize-alist R-customize-alist) (ess-write-to-dribble-buffer ;; for debugging only (format "\n(R): ess-dialect=%s, buf=%s, start-arg=%s\n current-prefix-arg=%s\n" ess-dialect (current-buffer) start-args current-prefix-arg)) (let* ((r-always-arg (if (or ess-microsoft-p (eq system-type 'cygwin)) "--ess " "--no-readline ")) (r-start-args (concat r-always-arg inferior-R-args " " ; add space just in case (if start-args (read-string (concat "Starting Args [other than `" r-always-arg "'] ? ")) nil))) ) ;;Micro$ ?: default-process-coding-system ;-breaks UTF locales on Unix: (if ess-microsoft-p (setq default-process-coding-system '(undecided-dos . undecided-dos))) (inferior-ess r-start-args) ;; -> .. (ess-multi ...) -> .. (inferior-ess-mode) .. ;;------------------------- (ess-write-to-dribble-buffer (format "(R): inferior-ess-language-start=%s\n" inferior-ess-language-start)) ;; can test only now that R is running: (if (ess-current-R-at-least '2.5.0) (progn (if ess-use-R-completion ;; use R's completion mechanism (pkg "rcompgen" or "utils") (progn ; nothing to happen here -- is all in ess-complete-object-name (ess-write-to-dribble-buffer "resetting completion to 'ess-R-complete-object-name") )) ;; problem with ess-help-command (let ((my-R-help-cmd (if (ess-current-R-at-least '2.10.0) "help" ;; else R version <= 2.9.2 "function(..., help_type) help(..., htmlhelp= (help_type==\"html\"))"))) (ess-eval-linewise (concat ".help.ESS <- " my-R-help-cmd) nil nil nil 'wait-prompt) )) ;; else R version <= 2.4.1 ;; for R <= 2.1.x : define baseenv() : (ess-eval-linewise "if(!exists(\"baseenv\", mode=\"function\")) baseenv <- function() NULL" nil nil nil 'wait-prompt);; solving "lines running together" ) (if inferior-ess-language-start (ess-eval-linewise inferior-ess-language-start nil nil nil 'wait-prompt)))) ;;;### autoload (defun R-mode (&optional proc-name) "Major mode for editing R source. See `ess-mode' for more help." (interactive) (setq ess-customize-alist R-customize-alist) ;;(setq imenu-generic-expression R-imenu-generic-expression) (ess-mode R-customize-alist proc-name) (if (fboundp 'ess-add-toolbar) (ess-add-toolbar)) ;; ECB needs seminatic stuff. ;; (if (featurep 'semantic) ;; (setq semantic-toplevel-bovine-table r-toplevel-bovine-table)) (if ess-imenu-use-S (progn (require 'ess-menu) (ess-imenu-R))) ;; MM: ^^^^^^^^^^^ should really use ess-imenu-mode-function from the ;; alist above! ;; ;; SJE: set up roxygen-fn. Perhaps we also need a hook here? (local-set-key "\C-c\C-o" 'ess-roxygen-fn) ) (fset 'r-mode 'R-mode) (defun ess-r-versions-create () "Generate the `M-x R-x.y' functions for starting other versions of R. On MS Windows, this works using `ess-rterm-version-paths'; otherwise, see `ess-r-versions' for strings that determine which functions are created. The result is a list of the new R defuns, if any, that were created. The defuns will normally be placed on the menubar and stored as `ess-r-versions-created' upon ESS initialisation." (if (not ess-r-versions) nil ;nothing to return ;; else, if ess-r-versions is non-nil, let's try to find those R versions. ;; This works by creating a temp buffer where the template function is ;; edited so that X.Y is replaced by the version name (let ((versions) (eval-buf (get-buffer-create "*ess-temp-r-evals*")) (r-versions-created) (template ;; This is the template function used for creating M-x R-X.Y. (concat "(defun R-X.Y (&optional start-args) \"Call R-X.Y, i.e., the R version 'R-X.Y' using ESS. This function was generated by `ess-r-versions-create'.\" (interactive \"P\") (let ((use-dialog-box nil);; Win-only: dialog box won't return a directory (inferior-R-program-name \"" (if ess-microsoft-p "Rterm" "R") "-X.Y\")) (R start-args))) " ) )) (save-excursion (set-buffer eval-buf) ;; clear the buffer. (delete-region (point-min) (point-max)) ;; Find which versions of R we want. Remove the pathname, leaving just ;; the name of the executable. (setq versions (if ess-microsoft-p ess-rterm-version-paths ;; ^^^^^^^^^^^^^^^^^^^^^^^ created in ;; ./ess-site.el at start ;; else (non-MS): (ess-uniq-list (mapcar 'file-name-nondirectory (apply 'nconc (mapcar 'ess-find-exec-completions ess-r-versions)))))) (ess-write-to-dribble-buffer (format "(R): ess-r-versions-create making M-x defuns for \n %s\n" (mapconcat 'identity versions "\n "))) (if (not ess-microsoft-p) (setq r-versions-created versions)) ;keep copy for returning at end. ;; Iterate over each string in VERSIONS, creating a new defun each time. (while versions (let* ((version (car versions)) (this-version version) (beg (point))) (setq versions (cdr versions)) (when ess-microsoft-p (setq version (file-name-nondirectory (ess-chop1 (file-name-directory (ess-chop1 (file-name-directory version))))) r-versions-created (cons version r-versions-created))) (insert template) (goto-char beg) (while (search-forward "R-X.Y" nil t) (replace-match version t t)) (when ess-microsoft-p (goto-char beg) (while (search-forward "Rterm-X.Y" nil t) (replace-match this-version t t))) (goto-char (point-max))) ) ;; buffer has now been created with defuns, so eval them! (eval-buffer) (kill-buffer eval-buf) ) r-versions-created))) (defvar ess-newest-R nil "Stores the newest version of R that has been found. Used as a cache, within ess-find-newest-R. Do not use this value directly, but instead call the function \\[ess-find-newest-R].") (defun ess-find-newest-R () "Find the newest version of R on the system. Once the value is found, cache it in the variable `ess-newest-R' for future use as finding the newest version of R can be potentially time-consuming." (or ess-newest-R (progn (message "Finding all versions of R on your system...") ;;(sleep-for 3) nil) (setq ess-newest-R (ess-newest-r (if ess-microsoft-p ess-rterm-version-paths (add-to-list 'ess-r-versions-created inferior-R-program-name)))))) (defun ess-check-R-program-name () "Check if `inferior-R-program-name' points to an executable version of R. If not, try to find the newest version of R elsewhere on the system, and update `inferior-R-program-name' accordingly." (unless (executable-find inferior-R-program-name) ;; need to check if we can find another name. (let ((newest (ess-find-newest-R))) (if newest (setq inferior-R-program-name newest) (message "Sorry, no version of R could be found on your system."))))) (defun R-newest (&optional start-args) "Find the newest version of R available, and run it. Subsequent calls to R-newest will run that version, rather than searching again for the newest version. Providing an optional prefix arg (C-u) will prompt for command line arguments." (interactive "P") (let ((rnewest (ess-find-newest-R))) (if (not rnewest) (error "No version of R could be found.") ;; Else: we have a working version of R. ;; Have to be careful to avoid recursion... (message (concat "Newest version of R is " rnewest)) (fset 'R-newest (intern (if ess-microsoft-p (file-name-nondirectory (substring (file-name-directory (substring (file-name-directory rnewest) 0 -1)) 0 -1)) rnewest))) ;;(fset 'R-newest (intern rnewest)) (R-newest start-args)))) ;; (ess-r-version-date "R-2.5.1") (ess-r-version-date "R-patched") ;; (ess-r-version-date "R-1.2.1") (ess-r-version-date "R-1.8.1") ;; Note that for R-devel, ver-string is something like ;; R version 2.6.0 Under development (unstable) (2007-07-14 r42234) ;; Antique examples are 'R 1.0.1 (April 14, 2000)' or 'R 1.5.1 (2002-06-17).' (defun ess-r-version-date (rver) "Return the date of the version of R named RVER. The date is returned as a date string. If the version of R could not be found from the output of the RVER program, \"-1\" is returned." (let (ver-string (date "-1")) (setq ver-string (shell-command-to-string (concat rver " --version"))) (when (string-match "R \\(version \\)?[1-9][^\n]+ (\\(2[0-9-]+\\)\\( r[0-9]+\\)?)" ver-string) (setq date (match-string 2 ver-string))) (cons date rver))) (defun ess-current-R-version () "Get the version of R currently running in the ESS buffer as a string" (ess-make-buffer-current) (car (ess-get-words-from-vector "as.character(getRversion())\n"))) (defun ess-current-R-at-least (version) "Is the version of R (in the ESS buffer) at least (\">=\") VERSION ? Examples: (ess-current-R-at-least '2.7.0) or (ess-current-R-at-least \"2.5.1\")" (ess-make-buffer-current) (string= "TRUE" (car (ess-get-words-from-vector (format "as.character(getRversion() >= \"%s\")\n" version))))) (defun ess-newest-r (rvers) "Check all the versions of RVERS to see which is the newest. Return the name of the newest version of R." (let ((rtimes (mapcar 'ess-r-version-date rvers))) ;; SJE: 2007-07-13 -- following line is a temp var to check that ;; the newest version of R is found correctly. (setq ess-temp-newest rtimes) (ess-find-newest-date rtimes))) ;; Test case for following defun: ;; (setq a '( ("2003-10-04" . "R-1.7") ;; ("2006-11-19" . "R-2.2") ;; ("2007-07-01" . "R-dev") ;; ("-1" . "R-broken") ;; ("2005-12-30" . "R-2.0"))) ;; (ess-find-newest-date a) (defun ess-find-newest-date (rvers) "Find the newest version of R given in the a-list RVERS. Each element of RVERS is a dotted pair (date . R-version), where date is given as e.g.\"2007-11-30\" so that we can compare dates as strings. If a date is listed as \"-1\", that version of R could not be found. If the value returned is nil, no valid newest version of R could be found." (let (new-r this-r (new-time "0")) (while rvers (setq this-r (car rvers) rvers (cdr rvers)) (when (string< new-time (car this-r)) (setq new-time (car this-r) new-r (cdr this-r)))) new-r)) (defun ess-find-rterm (&optional ess-R-root-dir) "Find the full path of all occurences of Rterm.exe under the ESS-R-ROOT-DIR. If ESS-R-ROOT-DIR is nil, construct it by looking for an occurence of Rterm.exe in the exec-path. If there are no occurences of Rterm.exe in the exec-path, then use `ess-program-files' (which evaluates to something like \"c:/progra~1/R/\" in English locales) which is the default location for the R distribution." (if (not ess-R-root-dir) (let ((Rpath (executable-find "Rterm"))) (setq ess-R-root-dir (expand-file-name (if Rpath (concat (file-name-directory Rpath) "../../") (concat ess-program-files "/R/")))) (ess-write-to-dribble-buffer (format "(ess-find-rterm): ess-R-root-dir = '%s'\n" ess-R-root-dir)) )) (when (file-directory-p ess-R-root-dir) ; otherwise file-name-all-.. errors (setq ess-R-root-dir (ess-replace-regexp-in-string "[\\]" "/" ess-R-root-dir)) (let ((R-ver (ess-drop-non-directories (ess-flatten-list (mapcar '(lambda (r-prefix) (file-name-all-completions r-prefix ess-R-root-dir)) (append '("rw") ess-r-versions)))))) (mapcar '(lambda (dir) (concat ess-R-root-dir (ess-replace-regexp-in-string "[\\]" "/" dir) "bin/Rterm.exe")) R-ver)))) ;; From Jim (James W.) MacDonald, based on code by Deepayan Sarkar, ;; originally named 'alt-ess-complete-object-name'. ;; Use rcompgen in ESS ;; Can be activated by something like ;; (define-key inferior-ess-mode-map "\t" 'ess-R-complete-object-name) (defun ess-R-complete-object-name () "Completion in R via R's completion utilities (formerly 'rcompgen'). To be used instead of ESS' completion engine for R versions >= 2.5.0 (or slightly older versions of R with an attached and working 'rcompgen' package)." (interactive) (ess-make-buffer-current) (let* ((comint-completion-addsuffix nil) (beg-of-line (save-excursion (comint-bol nil) (point))) (end-of-line (point-at-eol)) (line-buffer (buffer-substring beg-of-line end-of-line)) (NS (if (ess-current-R-at-least '2.7.0) "utils:::" "rcompgen:::")) (token-string ;; setup, including computation of the token (progn (ess-command (format (concat NS ".assignLinebuffer('%s')\n") line-buffer)) (ess-command (format (concat NS ".assignEnd(%d)\n") (- (point) beg-of-line))) (car (ess-get-words-from-vector (concat NS ".guessTokenFromLine()\n"))))) (possible-completions ;; compute and retrieve possible completions (progn (ess-command (concat NS ".completeToken()\n")) (ess-get-words-from-vector (concat NS ".retrieveCompletions()\n"))))) (or (comint-dynamic-simple-complete token-string possible-completions) 'none))) ;;;### autoload (defun Rnw-mode () "Major mode for editing Sweave(R) source. See `noweb-mode' and `R-mode' for more help." (interactive) (require 'ess-noweb);; << probably someplace else (noweb-mode 1); turn it on (noweb-set-doc-mode 'latex-mode) (noweb-set-code-mode 'R-mode) (run-hooks 'Rnw-mode-hook)) (fset 'Snw-mode 'Rnw-mode); just a synonym (for now or ever) (autoload 'ess-transcript-mode "ess-trns" "Major mode for editing S transcript files." t) (defun R-transcript-mode () "Does the right thing." (interactive) (ess-transcript-mode R-customize-alist)) (fset 'r-transcript-mode 'R-transcript-mode) (defun R-fix-T-F (&optional from quietly) "Fix T/F into TRUE and FALSE *cautiously*, i.e. not in comments and strings; starting from the current position (point)." (interactive "d\nP"); point and prefix (C-u) (save-excursion (goto-char from) (ess-rep-regexp "\\(\\([][=,()]\\|<-\\) *\\)T\\>" "\\1TRUE" 'fixcase nil (not quietly)) (goto-char from) (ess-rep-regexp "\\(\\([][=,()]\\|<-\\) *\\)F\\>" "\\1FALSE" 'fixcase nil (not quietly)))) ;; From: Sebastian Luque ;; To: ess-help@stat.math.ethz.ch ;; Date: Mon, 01 May 2006 19:17:49 -0500 ;; Without knowing how to tell R to use w3m from within Emacs, and after ;; switching to Konqueror's window for the millionth time, I wrote the ;; following function: ;; This emulates some of the functionality of RSiteSearch() and tests ok in ;; my system GNU Emacs 22.0.50.1 (i486-pc-linux-gnu, X toolkit, Xaw3d scroll ;; bars) of 2006-04-27 on pacem, modified by Debian. This has the benefit of ;; displaying results with whatever you've told browse-url to use; in my ;; case, w3m with the emacs-w3m package. ;; My elisp skills are rather poor, so comments and suggestions for ;; improvement are welcome. ;; -- ;; Seb ;; MM _FIXME_: This only works correctly for Emacs 22.0.50 (alpha) ;; for 21.x it has problems in the (completing-read-multiple .) ;; at the end (defun R-site-search (string) "Search the R archives for STRING, using default criteria. If called with a prefix, options are available for 1) matches per page, 2) sections of the archives to search (separated by value of `crm-default-separator'), 3) for displaying results in long or short formats, and 4) for sorting by any given field. Completion is available for supplying options." (interactive "sSearch string: ") (let ((site "http://search.r-project.org/cgi-bin/namazu.cgi?query=") (okstring (replace-regexp-in-string " +" "+" string))) (if current-prefix-arg (let ((mpp (concat "&max=" (completing-read "Matches per page: " '(("20" 1) ("30" 2) ("40" 3) ("50" 4) ("100" 5))))) (format (concat "&result=" (completing-read "Format: " '("normal" "short") nil t "normal" nil "normal"))) (sortby (concat "&sort=" (completing-read "Sort by: " '(("score" 1) ("date:late" 2) ("date:early" 3) ("field:subject:ascending" 4) ("field:subject:decending" 5) ("field:from:ascending" 6) ("field:from:decending" 7) ("field:size:ascending" 8) ("field:size:decending" 9)) nil t "score" nil "score"))) (restrict (concat "&idxname=" (mapconcat 'identity (completing-read-multiple "Limit search to: " '(("Rhelp02a" 1) ("functions" 2) ("docs" 3) ("Rhelp01" 4)) nil t "Rhelp02a,functions,docs" nil "Rhelp02a,functions,docs") "&idxname=")))) (browse-url (concat site okstring mpp format sortby restrict))) ;; else: without prefix use defaults: (browse-url (concat site okstring "&max=20&result=normal&sort=score" "&idxname=Rhelp02a&idxname=functions&idxname=docs"))))) ; provides (provide 'essd-r) ; Local variables section ;;; This file is automatically placed in Outline minor mode. ;;; The file is structured as follows: ;;; Chapters: ^L ; ;;; Sections: ;;*;; ;;; Subsections: ;;;*;;; ;;; Components: defuns, defvars, defconsts ;;; Random code beginning with a ;;;;* comment ;;; Local variables: ;;; mode: emacs-lisp ;;; outline-minor-mode: nil ;;; mode: outline-minor ;;; outline-regexp: "\^L\\|\\`;\\|;;\\*\\|;;;\\*\\|(def[cvu]\\|(setq\\|;;;;\\*" ;;; End: ;;; essd-r.el ends here