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;;; ess.el --- Emacs Speaks Statistics: statistical programming within Emacs
;; Copyright (C) 1989--1996 Bates, Kademan, Ritter and Smith
;; Copyright (C) 1997--2010 A.J. Rossini, Richard M. Heiberger, Martin
;; Maechler, Kurt Hornik, Rodney Sparapani, and Stephen Eglen.
;; Copyright (C) 2011--2015 A.J. Rossini, Richard M. Heiberger, Martin Maechler,
;; Kurt Hornik, Rodney Sparapani, Stephen Eglen and Vitalie Spinu.
;; Author: Doug Bates
;; Ed Kademan
;; Frank Ritter
;; David Smith
;; Created: October 14, 1991
;; Maintainer: ESS-core <ESS-core@r-project.org>
;; Keywords: statistics, languages
;; 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.
;;
;; A copy of the GNU General Public License is available at
;; http://www.r-project.org/Licenses/
;;; Commentary:
;; PURPOSE
;;
;; Interface to the S, SAS, and XLisp dialects of statistical
;; programming languages, with potential extensions to other
;; languages. Designed to be extendable to most other interactive
;; statistical programming situations.
;; BRIEF OVERVIEW
;;
;; Supports structured editing of S, SAS, and XLisp (statistics
;; programming languages) functions that are integrated with a
;; running process in a buffer.
;; THE ESS MAILING LIST
;;
;; There is an informal mailing list for discussions of ESS. Alpha
;; and beta releases of ESS are also announced here. Send mail
;; to ess-help-request@r-project.org to join.
;; OVERVIEW OF ESS
;;
;; S is a statistics programming language developed at Bell Labs
;; particularly suited for descriptive and exploratory statistics.
;; s-mode is built on top of comint (the general command interpreter
;; mode written by Olin Shivers), and so comint.el (or comint.elc)
;; should be either loaded or in your load path when you invoke it.
;;
;; Aside from the general features offered by comint such as
;; command history editing and job control, inferior S mode
;; allows you to dump and load S objects into and from external
;; files, and to display help on functions. It also provides
;; name completion while you do these. For more detailed
;; information see the documentation strings for inferior-ess,
;; inferior-ess-mode, ess-mode, and comint-mode. There are also
;; many variables and hooks available for customizing (see
;; the variables below that have document strings that start
;; with an "*").
;; INSTALLATION
;; See README and S-site for details.
;; GETTING RELEASES OF ESS
;; ===> http://ess.r-project.org
;;
;; CREDITS.
;; Thanks to shiba@shun.isac.co.jp (Ken'ichi "Modal" Shibayama) for
;; the indenting code.
;; Thanks also to maechler@stat.math.ethz.ch (Martin Maechler) for
;; suggestions and bug fixes.
;; ess-eval-line-and-step is based on a function by Rod Ball
;; (rod@marcam.dsir.govt.nz)
;; Also thanks from David Smith to the previous authors for all their
;; help and suggestions.
;; And thanks from Richard M. Heiberger, Kurt Hornik, Martin
;; Maechler, and A.J. Rossini to David Smith.
;; BUG REPORTS
;; Please report bugs to ess-bugs@r-project.org
;; Comments, suggestions, words of praise and large cash donations
;; are also more than welcome, but should generally be split between
;; all authors :-).
;;; Code:
;;*;; Requires and autoloads
;;;=====================================================
;;;
(require 'easymenu)
(if (or window-system
noninteractive ; compilation!
)
(require 'font-lock))
(require 'ess-compat)
(require 'ess-custom)
(require 'ess-mode)
(require 'ess-inf)
(require 'cl)
; ess-mode: editing S/R/XLS/SAS source
(autoload 'inferior-ess "ess-inf"
"Run [inferior-ess-program], an ess process, in an Emacs buffer" t)
(autoload 'ess-dump-object-into-edit-buffer "ess-mode"
"Edit an S object." t)
(autoload 'ess-parse-errors "ess-mode"
"Jump to the last error generated from a sourced file." t)
(autoload 'ess-load-file "ess-inf" "Source a file into S.")
(autoload 'ess-inside-string-or-comment-p "ess-utils"
"Non-nil, if inside string or comment." t)
(autoload 'ess-inside-string-p "ess-utils" "Non-nil if inside string." t)
(autoload 'ess-do-auto-fill "ess-utils" "substitute for \\[do-auto-fill]." t)
(autoload 'ess-rep-regexp "ess-utils" "Replace, but not in string/comment." t)
(autoload 'ess-time-string "ess-utils" "Return time-stamp string." t)
(autoload 'ess-nuke-trailing-whitespace "ess-utils"
"Maybe get rid of trailing blanks." t)
; ess-transcript-mode: editing ``outputs'
(autoload 'ess-transcript-mode "ess-trns"
"Major mode for editing S transcript files." t)
(autoload 'ess-display-help-on-object "ess-help"
"Display help on an S object." t)
(defalias 'ess-help 'ess-display-help-on-object)
(autoload 'ess-goto-info "ess-help"
"Jump to the relevant section in the `ess-mode' manual." t)
(autoload 'ess-submit-bug-report "ess-help"
"Submit a bug report on the `ess-mode' package." t)
;;==> ess-inf.el has its OWN autoload's !
; Miscellaneous "ESS globals"
(defun ess-version-string ()
(let* (;;(svn-fname (concat ess-etc-directory "SVN-REVISION"))
;; (svn-rev
;; (when (file-exists-p svn-fname)
;; ;; then it has two lines that look like
;; ;; |Revision: 4803
;; ;; |Last Changed Date: 2012-04-16
;; (with-current-buffer (find-file-noselect svn-fname)
;; (goto-char (point-min))
;; (when (re-search-forward "Revision: \\(.*\\)\n.*: \\(.*\\)" nil t)
;; (concat "svn: " (match-string 1) " (" (match-string 2) ")")))))
(ess-dir (file-name-directory ess-lisp-directory)) ; if(<from source>) the top-level 'ess/'
(is-release (file-exists-p (concat ess-etc-directory ".IS.RELEASE")))
(rel-string (if is-release "Released "))
(git-ref-fn (concat ess-dir ".git/HEAD"))
(git-ref (when (file-exists-p git-ref-fn)
(with-current-buffer (find-file-noselect git-ref-fn)
(goto-char (point-min))
(when (re-search-forward "ref: \\(.*\\)\n" nil t)
(match-string 1)))))
(git-fname (if git-ref
(concat ess-dir ".git/" git-ref)
;; for release
(concat ess-etc-directory "git-ref")))
(git-rev (when (file-exists-p git-fname)
(with-current-buffer (find-file-noselect git-fname)
(goto-char (point-min))
(concat "git: "(buffer-substring 1 (point-at-eol))))))
(elpa-fname (concat ess-dir "ess-pkg.el"))
(elpa-rev (when (file-exists-p elpa-fname)
;; get it from ELPA dir name, (probably won't work if installed manually)
(concat "elpa: "
(replace-regexp-in-string "ess-" ""
(file-name-nondirectory
(substring ess-dir 1 -1)))))))
;; set the "global" ess-revision:
(setq ess-revision (format "%s%s%s"
(or rel-string "") ;;(or svn-rev "")
(or git-rev "")
(or elpa-rev "")))
(when (string= ess-revision "")
(setq ess-revision "<unknown>"))
(concat ess-version " [" ess-revision "]")))
(defun ess-version ()
(interactive)
(message (format "ess-version: %s (loaded from %s)"
(ess-version-string)
(file-name-directory ess-lisp-directory))))
;;; Set up for menus, if necessary
;;; --> is done in ess-mode.el, ess-inf.el, etc
; ESS yank
(defun ess-yank-cleaned-commands ()
"Yank and strip the code, leaving only (R/S/Lsp/..) commands.
Deletes any lines not beginning with a prompt, and then removes
the prompt from those lines that remain.
Invoke this command with C-u C-u C-y."
(setq yank-window-start (window-start))
(let ((beg (point)))
(push-mark beg)
(setq this-command t)
(insert-for-yank (current-kill 0))
(ess-transcript-clean-region beg (point) nil)
(if (eq (point) beg)
(message "No commands found"))
(if (eq this-command t)
(setq this-command 'yank))
))
(defun ess-yank (&optional ARG)
"With double prefix (C-u C-u) call `ess-yank-cleaned-commands"
(interactive "*P")
(if (equal '(16) ARG)
(ess-yank-cleaned-commands)
(let* ((remapped (command-remapping 'yank (point)))
(command (cond ((eq remapped 'ess-yank) 'yank)
((null remapped) 'yank)
(t remapped))))
(funcall command ARG))))
(put 'ess-yank 'delete-selection 'yank)
; ESS Completion
(defun ess-completing-read (prompt collection &optional predicate
require-match initial-input hist def)
"Read a string in the minibuffer, with completion.
Use `ido-completing-read' if IDO interface is present, or fall
back on classical `completing-read' otherwise. Meaning of
arguments is as in `completing-read' (PROMPT is automatically
suffixed with ': ' and (default %s) when needed). If HIST
is null use `ess--completing-hist' as history.
See also `ess-use-ido'.
"
(let ((use-ido (and ess-use-ido (featurep 'ido))))
(setq hist (or hist 'ess--completing-hist))
(when (and def (not use-ido)) ;; ido places in front and highlights the default
(setq prompt (format "%s(default %s)" prompt def)))
(setq prompt (concat prompt ": "))
(if use-ido
(let ((reset-ido (and use-ido (not ido-mode))) ;people not using ido but having it)
(ido-current-directory nil)
(ido-directory-nonreadable nil)
(ido-directory-too-big nil)
(ido-context-switch-command 'ignore)
(ido-enable-flex-matching ess-ido-flex-matching) ;it's fast and useful, may be get into options
(ido-choice-list (copy-sequence collection)) ;ido removes the match (reported)
sel)
(unwind-protect
(progn
(ido-init-completion-maps)
(add-hook 'minibuffer-setup-hook 'ido-minibuffer-setup)
(add-hook 'choose-completion-string-functions 'ido-choose-completion-string)
(setq sel (ido-read-internal 'list prompt hist def require-match initial-input))
(when hist ;; ido does not push into hist the whole match if C-SPC or RET is used (reported)
(unless (string= sel (car (symbol-value hist)))
(set hist (cons sel (symbol-value hist))))))
(when reset-ido
(remove-hook 'minibuffer-setup-hook 'ido-minibuffer-setup)
(remove-hook 'choose-completion-string-functions 'ido-choose-completion-string)))
sel)
;; else usual completion
(when (and (featurep 'xemacs) ;; xemacs workaround
(not (listp (car collection))))
(setq collection (mapcar 'list collection)))
(completing-read prompt collection predicate require-match initial-input hist def)
)))
(defun ess-load-extras (&optional inferior)
"Load all the extra features depending on custom settings."
(let ((mode (if inferior 'inferior-ess-mode 'ess-mode))
(isR (string-match "^R" ess-dialect)))
;; auto-complete
(when (and (boundp 'ac-sources)
(if inferior
(eq ess-use-auto-complete t)
ess-use-auto-complete))
(add-to-list 'ac-modes mode)
;; files should be in front; ugly, but needed
(when ess-ac-sources
(setq ac-sources
(delq 'ac-source-filename ac-sources))
(mapcar (lambda (el) (add-to-list 'ac-sources el))
ess-ac-sources)
(add-to-list 'ac-sources 'ac-source-filename)))
;; company
(when (and (boundp 'company-backends)
(if inferior
(eq ess-use-company t)
ess-use-company))
(when ess-company-backends
(set (make-local-variable 'company-backends)
(copy-list (append ess-company-backends company-backends)))
(delq 'company-capf company-backends)))
;; eldoc)
(require 'eldoc)
(when (and ess-eldoc-function ;; if mode provide this, it suports eldoc
(or (and (not inferior) ess-use-eldoc)
(and inferior (eq ess-use-eldoc t))))
(when (> eldoc-idle-delay 0.4) ;; default is too slow for paren help
(set (make-local-variable 'eldoc-idle-delay) 0.1))
(set (make-local-variable 'eldoc-documentation-function) ess-eldoc-function)
(turn-on-eldoc-mode))
;; tracebug
(when (and ess-use-tracebug inferior isR)
(ess-tracebug 1))))
;; not in use since 2004
;; (defun ess-load-object-name-db-file ()
;; "Load object database file if present, mention if not."
;; (if (string= ess-language "S")
;; (progn
;; (make-local-variable 'ess-object-name-db)
;; (condition-case ()
;; (load ess-object-name-db-file)
;; (error
;; ;;(message "%s does not exist. Consider running ess-create-object-name-db."
;; ;; ess-object-name-db-file)
;; ;; (ding)
;; (sit-for 1))))))
;;; xemacs process-put and process-get workarounds:
;;; !!!! remove this when xemacs starts supporting them!!!
(when (featurep 'xemacs)
(defvar process-plist-map (make-hash-table :test 'eq :weakness 'key)
"Property list information for process, when XEmacs doesn't provide this.
See `process-plist' and `set-process-plist'.")
(defun-when-void process-plist (process)
"Return the property list of PROCESS."
(check-argument-type #'processp process)
(gethash process process-plist-map))
(defun-when-void set-process-plist (process plist)
"Set the property list of PROCESS to PLIST."
(check-argument-type #'processp process)
(check-argument-type #'valid-plist-p plist)
(puthash process plist process-plist-map))
(defun-when-void process-get (process propname)
"Return the value of PROCESS' PROPNAME property.
This is the last value stored with `(process-put PROCESS PROPNAME VALUE)'."
(plist-get (process-plist process) propname))
(defun-when-void process-put (process propname value)
"Change PROCESS' PROPNAME property to VALUE.
It can be retrieved with `(process-get PROCESS PROPNAME)'."
(set-process-plist process
(plist-put (process-plist process) propname value)))
)
;;; Running these must be done "every time" before use, since
;;; they depend on a customizable variable.
;; trying different viewers; thanks to an original patch for
;; ess-swv.el from Leo <sdl@web.de> :
(defun ess-get-ps-viewer ()
"Get external PostScript viewer to be used from ESS.
Use `ess-ps-viewer-pref' when that is executably found by \\[executable-find].
Otherwise try a list of fixed known viewers."
(file-name-nondirectory
(or (and ess-ps-viewer-pref ; -> ./ess-custom.el
(executable-find ess-ps-viewer-pref))
(executable-find "gv")
(executable-find "evince")
(executable-find "kghostview"))))
(defun ess-get-pdf-viewer ()
"Get external PDF viewer to be used from ESS.
Use `ess-pdf-viewer-pref' when that is executably found by \\[executable-find].
Otherwise try a list of fixed known viewers.
"
(let ((viewer (or ess-pdf-viewer-pref
;; (and (stringp ess-pdf-viewer-pref) ; -> ./ess-custom.el
;; (executable-find ess-pdf-viewer-pref))
(executable-find "evince")
(executable-find "kpdf")
(executable-find "okular")
(executable-find "xpdf")
(executable-find "acroread")
(executable-find "xdg-open")
;; this one is wrong, (ok for time being as it is used only in swv)
(car (ess-get-words-from-vector
"getOption(\"pdfviewer\")\n"))
)))
(when (stringp viewer)
(setq viewer (file-name-nondirectory viewer)))
viewer))
; Buffer local customization stuff
;; Parse a line into its constituent parts (words separated by
;; whitespace). Return a list of the words.
;; Taken from rlogin.el, from the comint package, from XEmacs 20.3.
(defun ess-line-to-list-of-words (line)
(if (listp line)
line
(let ((list nil)
(posn 0))
;; (match-data (match-data)))
(while (string-match "[^ \t\n]+" line posn)
(setq list (cons (substring line (match-beginning 0) (match-end 0))
list))
(setq posn (match-end 0)))
(store-match-data (match-data))
(nreverse list))))
(defun ess-write-to-dribble-buffer (text)
"Write TEXT to dribble ('*ESS*') buffer."
(unless (buffer-live-p ess-dribble-buffer)
;; ESS dribble buffer must be re-created.
(setq ess-dribble-buffer (get-buffer-create "*ESS*")))
(let (deactivate-mark)
(with-current-buffer ess-dribble-buffer
(goto-char (point-max))
(insert-before-markers text))))
;; Shortcut to render "dribbling" statements less cluttering:
(defun ess-if-verbose-write (text)
"Write TEXT to dribble buffer ('*ESS*') only *if* `ess-verbose'."
(if ess-verbose (ess-write-to-dribble-buffer text)))
(defvar ess--make-local-vars-permenent nil
"If this varialbe is non-nil in a buffer make all variable permannet.
Used in noweb modes.")
(make-variable-buffer-local 'ess--make-local-vars-permenent)
(put 'ess--make-local-vars-permenent 'permanent-local t)
(defun ess-setq-vars-local (alist &optional buf)
"Set language variables from ALIST, in buffer BUF, if desired."
(if buf (set-buffer buf))
;; (setq alist (reverse alist)) ;; It should really be in reverse order;
(mapc (lambda (pair)
(make-local-variable (car pair))
(set (car pair) (eval (cdr pair)))
(when ess--make-local-vars-permenent
(put (car pair) 'permanent-local t)) ;; hack for Rnw
)
alist)
(ess-write-to-dribble-buffer
(format "(ess-setq-vars-LOCAL): language=%s, dialect=%s, buf=%s, comint..echoes=%s, comint..sender=%s\n"
ess-language ess-dialect buf comint-process-echoes comint-input-sender)))
(defun ess-setq-vars-default (alist &optional buf)
"Set language variables from ALIST, in buffer BUF, if desired."
(ess-write-to-dribble-buffer
(format "ess-setq-vars-default 0: ess-language=%s, -dialect=%s, buf=%s, comint..echoes=%s, comint..sender=%s\n"
ess-language ess-dialect buf comint-process-echoes comint-input-sender))
(if buf (set-buffer buf))
(mapc (lambda (pair)
(set-default (car pair) (eval (cdr pair))))
alist)
(ess-write-to-dribble-buffer
(format "ess-setq-vars-default 1: ess-language=%s, -dialect=%s, buf=%s, comint..echoes=%s, comint..sender=%s\n"
ess-language ess-dialect buf comint-process-echoes comint-input-sender))
)
;;; versions thanks to Barry Margolin <barmar@bbnplanet.com>.
;;; unfortunately, requires 'cl. Whoops.
;;(defun ess-setq-vars (var-alist &optional buf)
;; "Set language variables from alist, in buffer `buf', if desired."
;; (if buf (set-buffer buf))
;; (dolist (pair var-alist)
;; (set (car pair) (eval (cdr pair))))
;; (ess-write-to-dribble-buffer
;; (format "(ess-setq-vars): ess-language=%s, buf=%s \n"
;; ess-language buf)))
;;(defun ess-setq-vars-default (var-alist &optional buf)
;; "Set language variables from alist, in buffer `buf', if desired."
;; (if buf (set-buffer buf))
;; (dolist (pair var-alist)
;; (set-default (car pair) (eval (cdr pair))))
;; (ess-write-to-dribble-buffer
;; (format "(ess-setq-vars-default): ess-language=%s, buf=%s \n"
;; ess-language buf)))
;; Toby Speight <Toby.Speight@ansa.co.uk>
;;> ;; untested
;;> (let ((l R-customize-alist)) ; or whatever
;;> (while l
;;> (set (car (car l)) (cdr (car l))) ; set, not setq!
;;> (setq l (cdr l))))
;;
;;
;;If they are to be buffer-local, you may need to
;;
;;> ;; untested
;;> (set (make-local-variable (car (car l))) (cdr (car l)))
;;
;; Erik Naggum <erik@naggum.no>
;;
;;(mapcar (lambda (pair) (set (car pair) (cdr pair)))
;; R-customize-alist)
;;
;;if you want to evaluate these things along the way, which it appears that
;;you want, try:
;;
;;(mapcar (lambda (pair) (set (car pair) (eval (cdr pair))))
;; R-customize-alist)
;; jsa@alexandria.organon.com (Jon S Anthony)
;;(mapcar (lambda (x)
;; (set-variable (car x) (cdr x)))
;; R-customize-alist)
; Run load hook and provide package
(run-hooks 'ess-mode-load-hook)
(provide 'ess)
; 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
;;; mode: outline-minor
;;; outline-regexp: "\^L\\|\\`;\\|;;\\*\\|;;;\\*\\|(def[cvu]\\|(setq\\|;;;;\\*"
;;; End:
;;; ess.el ends here