Merge branch 'trunk'

ChangeLog

@@ -1,3 +1,7 @@
+2013-12-07  ESS Maintainers <ESS-core@r-project.org>
+
+  * Version 13.09-1 released.
+
 2013-09-27  ESS Maintainers <ESS-core@r-project.org>
 
   * Version 13.09 released.

doc/newfeat.texi

@@ -3,39 +3,39 @@
 
 Changes / Selected Bug Fixes in 13.09-1:
 @itemize @bullet
-@item ess-remote and TRAMP: R suport code is now downloaded in binary form, instead
+@item ess-remote and TRAMP: R support code is now downloaded in binary form instead
 of being injected from local machine. The R code is stored in
-@code{~/.config/ESSR/} directory on the remote machine.
-@item TRAMP: PAGER environment variable is now correctly set to @code{inferior-ess-pager}.
-@item retrieval of help topics on remote machines was fixed
+@code{~/.config/ESSR/} directory on the remote machine
+@item TRAMP: PAGER environment variable is now correctly set to @code{inferior-ess-pager}
+@item retrieval of help topics on remote machines is fixed
 @item org-babel: source references of R code executed from org files correctly point
 to source references in original org files (version 8.2.1 or higher of
 org-mode is required for this feature)
 @item @code{ess-execute} is now bound to @kbd{C-c C-e C-e} in @code{ess-extra-map}.
 @item completion works again in @code{ess-execute}
-@item @ESS{[R]} @code{head} and @code{tail} methods were replaced by @code{htsummary} in
+@item @ESS{[R]}: @code{head} and @code{tail} methods were replaced by @code{htsummary} in
 @code{ess-R-describe-object-at-point-commands}
-@item @ESS{[roxygen]} evaluation commands now work in roxygen blocks.
-Leading comments are automatically removed before the evaluation.
+@item @ESS{[roxygen]}: evaluation commands now work in roxygen blocks.
+Leading comments are automatically removed before the evaluation
 @item @ESS{[transcript]}: 'Clean Region' now works with multiline statements;
- @code{ess-transcript-clean-region} etc, now also correctly treat
- multiline statements, i.e., it no longer forgets the lines typically
- preceded by ``+ ''.
-@item @ESS{[SAS]} Three features/fixes with special thanks to Matthew Fidler
+ @code{ess-transcript-clean-region} etc. correctly treat
+ multiline statements, i.e., no longer forgets the lines typically
+ preceded by '+'
+@item @ESS{[SAS]}: Three features/fixes with special thanks to Matthew Fidler
 @uref{https://github.com/emacs-ess/ESS/pulls/mlf176f2,
 https://github.com/emacs-ess/ESS/pulls/mlf176f2}. Turn on SAS log mode
-and SAS listing mode when appropriate.  Indent comments more
-appropriately. Indent CARDS more appropriately.
+when appropriate.  Indent comments and CARDS statement more appropriately. 
 @item @ESS{[SAS]}: @code{ess-sas-edit-keys-toggle} default returns to @code{nil}
-@item @ESS{[R]} support for @code{prettify-symbols-mode}
-A contribution of Rüdiger Sonderfeld @uref{https://github.com/emacs-ess/ESS/pull/65}
-@item @ESS{[SWV]} knitr now evaluates in the current frame
-@item @ESS{[developer]} ess-developer doesn't kill open DESCRIPTION files anymore
-@item @ESS{[roxygen]} @code{ess-roxy-preview-HTML} is now on @kbd{C-c C-o C-w} and
- @code{ess-roxy-preview-text} is now on @code{C-c C-o C-t}.
+@item @ESS{[R]}: support for @code{prettify-symbols-mode}: 
+contribution from Rudiger Sonderfeld @uref{https://github.com/emacs-ess/ESS/pull/65}
+@item @ESS{[SWV]}: knitr now evaluates in the current frame
+@item @ESS{[developer]}: ess-developer doesn't kill open DESCRIPTION files anymore
+@item @ESS{[roxygen]}: @code{ess-roxy-preview-HTML} is now on @kbd{C-c C-o C-w} and
+ @code{ess-roxy-preview-text} is now on @code{C-c C-o C-t}
 @item @ESS{}: installation with @code{make install} was simplified and should work 
 out of the box on most *nix systems
-@item @ESS{} installation instructions in ESS documentation were considerably simplified.
+@item @ESS{} installation instructions simplified
+@item fixed font-lock bug introduced in 13.09 that was causing very slow process output
 @end itemize
 
 Changes/New Features in 13.09:

etc/ESSR/R/developer.R

@@ -9,15 +9,13 @@
 ## Otherwise R will call the registered (i.e. cached) S3 method instead of the
 ## new method that ess-developer inserted in the package environment.
 
-.essDev_differs <- function(f1, f2)
-    {
-        if (is.function(f1) && is.function(f2)){
-            !(identical(body(f1), body(f2)) && identical(args(f1), args(f2)))
-        }else
-            !identical(f1, f2)
-    }
+.essDev.eval <- function(string, package, file = tempfile("ESSDev")){
+    cat(string, file = file)
+    on.exit(file.remove(file))
+    .essDev_source(file,, package = package)
+}
 
-.essDev_source <- function (source, expr, package = "")
+.essDev_source <- function(source, expr, package = "")
     {
         ## require('methods')
         oldopts <- options(warn = 1)
@@ -279,3 +277,11 @@
         all(out)
     }
 }
+
+
+.essDev_differs <- function(f1, f2) {
+    if (is.function(f1) && is.function(f2)){
+        !(identical(body(f1), body(f2)) && identical(args(f1), args(f2)))
+    }else
+        !identical(f1, f2)
+}

etc/ESSR/VERSION

@@ -1 +1 @@
-1.1.3
+1.1.4

etc/slow-long-output.R

@@ -15,9 +15,17 @@ system.time(print(y))
 ##  user  system elapsed 
 ## 0.059   0.010   0.070  -- MM@lynne R CMD BATCH
 ##  user  system elapsed 
+## 0.120   0.138   3.225 (+/- 0.2) -- MM@lynne ESS 13.09-1 [svn: 5930]
+##---
 ## 0.124   0.097  52.540  -- MM@lynne ESS svn r 5909; incl font-locking, tracebug
 ## 0.128   0.080  57.305       ditto
 ## 0.139   0.088  54.770  -- sfs@lynne ESS 13.09 (emacs 24.3.1 GTK+)
+## --
+## 0.102   0.075   4.685  -- MM@lynne ESS 5.14 (emacs 24.3.1 incl font-lock!)
+## 0.091   0.078   4.683  --     "    ESS 12.04-4 [rev. 4896 (2012-06-07)]
+## 0.123   0.063   4.638  --     "    ESS 12.09-2 [rev. 5395 (2013-01-10)]
+## 0.117   0.118   3.358  --     "    ESS 13.05   [rev. 5574 (2013-05-14)]
+##                 ^^^^^ clearly a bit faster !
 
 set.seed(23456)
 y <- mkCh(50000)
@@ -26,6 +34,10 @@ system.time(print(y))
 ## 0.255    0.089    0.345  -- BATCH MM@lynne
 ## 0.685    0.369 1664.557  -- MM@lynne ESS svn r 5909 ...
 ## 0.760    0.398 1643.608  -- ..@lynne ESS 13.09
+## 0.590    0.510   33.349  --     "    ESS 13.05   [rev. 5574 (2013-05-14)]
+## 0.565    0.548   28.251	"	 "	
+## 0.598    0.450   27.804 	"	 "
+
 
 ## Don't even think of trying this with ESS, currently:
 y <- mkCh(200000)

lisp/ChangeLog

@@ -1,3 +1,9 @@
+2013-12-05  Rodney Sparapani  <rsparapa@mcw.edu>
+
+	* ess-sas-a.el (ess-sas-edit-keys-toggle): the default returns
+	to nil; indentation has improved somewhat and will probably
+	improve a bit more in the near future
+
 2013-10-19  Martin Maechler  <maechler@stat.math.ethz.ch>
 
 	* ess-trns.el (ess-transcript-clean-region): use t and nil, not 1

lisp/Makefile

@@ -70,15 +70,15 @@ install: dist
 	-$(INSTALLDIR) $(LISPDIR)
 	$(INSTALL) ChangeLog *.elc $(LISPDIR)
 	export J; for I in *.elc; do J=$$I; $(INSTALL) `basename $$J .elc`.el $(LISPDIR); done
-	if [ -n "$(SITELISP)" ] ; \
+	if [ -n "$(SITELISP)" -a ! -f "$(SITELISP)/ess-site.el" ] ; \
 	then \
-		ln -sf $(LISPDIR)/ess-site.el $(SITELISP)/ess-site.el ; \
+		ln -s $(LISPDIR)/ess-site.el $(SITELISP)/ess-site.el ; \
 	fi;
 #	test "$(LISPDIR)" = "." || $(INSTALL) *.elc $(LISPDIR)
 
 uninstall:
 	-cd $(LISPDIR) && $(UNINSTALL) ChangeLog *.elc *.el
-	if [ -n "$(SITELISP)" ] ; \
+	if [ -n "$(SITELISP)" -a -f "$(SITELISP)/ess-site.el" ] ; \
 	then \
 		cd $(SITELISP) && $(UNINSTALL) ess-site.el ; \
 	fi;

lisp/ess-developer.el

@@ -221,11 +221,10 @@ otherwise call devSource."
       (ess-developer-devSource beg end package message))))
 
 (defun ess-developer-devSource (beg end package &optional message)
-  (let* ((ess-load-command
-          (format ".essDev_source(source='%s',package='%s')" "%s" package))
-         (ess-load-visibly-noecho-command ess-load-command)
-         ;; don't want string evaluation
-         ess-eval-command ess-eval-visibly-noecho-command)
+  (let* ((ess-eval-command
+          (format ".essDev.eval('%s', package='%s', file='%s')" "%s" package "%f"))
+         (ess-eval-visibly-command ess-eval-command)
+         (ess-eval-visibly-noecho-command ess-eval-command))
     (if message (message message))
     (ess-developer--command (ess--make-source-refd-command beg end)
                             'ess-developer--propertize-output)))

lisp/ess-inf.el

@@ -308,7 +308,7 @@ Alternatively, it can appear in its own frame if
 
             ;; don't font-lock strings over process prompt
             (set (make-local-variable 'syntax-begin-function)
-                 #'inferior-ess-goto-last-prompt)
+                 #'inferior-ess-goto-last-prompt-if-close)
             (set (make-local-variable 'font-lock-fontify-region-function)
                  #'inferior-ess-fontify-region)
 
@@ -354,11 +354,21 @@ Default depends on the ESS language/dialect and hence made buffer local")
 ;;; local to the ESS process buffer. If required, these variables should
 ;;; be accessed with the function ess-get-process-variable
 
-(defun inferior-ess-goto-last-prompt ()
-  (let ((paragraph-start comint-prompt-regexp))
-    (forward-paragraph -1)
-    ;; (comint-skip-prompt)
-    (point)))
+
+(defun inferior-ess-goto-last-prompt-if-close ()
+  "If any prompt has been found on current line, go to previous primary prompt and return the position.
+Otherwise stay at current position and return nil "
+
+  (let ((new-point (save-excursion
+                     (beginning-of-line)
+                     (if (looking-at inferior-ess-primary-prompt)
+                         (point)
+                       (when  (and inferior-ess-secondary-prompt
+                                   (looking-at inferior-ess-secondary-prompt))
+                         (re-search-backward (concat "^" inferior-ess-primary-prompt))
+                         (point))))))
+    (when new-point
+      (goto-char new-point))))
 
 (defun inferior-ess-fontify-region (beg end &optional verbose)
   "Fontify output by output within the beg-end region to avoid
@@ -367,7 +377,8 @@ fontification spilling over prompts."
 	 (inhibit-point-motion-hooks t)
          (font-lock-dont-widen t)
          (buff (current-buffer))
-         (pos (inferior-ess-goto-last-prompt)) ; expand to last prompt
+         (pos (or (inferior-ess-goto-last-prompt-if-close)
+                  beg))
          (pos2))
     (with-silent-modifications
       ;; (dbg pos end)
@@ -381,8 +392,7 @@ fontification spilling over prompts."
           ;; (redisplay)
           ;; (sit-for 1)
           (font-lock-default-fontify-region pos pos2 verbose))
-        (setq pos pos2)))
-    ))
+        (setq pos pos2)))))
 
 (defun ess-gen-proc-buffer-name:simple (proc-name)
   "Function to generate buffer name by wrapping PROC-NAME in *proc-name*"
@@ -2609,33 +2619,6 @@ A negative prefix argument gets the objects for that position
                               ")\n")))
     (ess-execute the-command invert "S objects" the-message)))
 
-;;;; S4 Version
-;;;; soup-up the interactive usage: allow modifications to a default pattern
-;;(defun ess-execute-objects (posn)
-;;  "Send the `inferior-ess-objects-command' to the ESS process.
-;;No prefix argument uses position 1 and pattern inferior-ess-objects-pattern.
-;;A nonnegative prefix gets objects for that position and prompts for
-;;  the pattern.
-;;A negative prefix also toggles ess-execute-in-process-buffer."
-;;  (interactive "P")
-;;  (ess-make-buffer-current)
-;;  (let* ((num-arg (if (listp posn) 1
-;;                  (prefix-numeric-value posn)))
-;;       (the-posn (if (< num-arg 0) (- num-arg) num-arg))
-;;       (invert (< num-arg 0))
-;;       (pattern (if current-prefix-arg (read-string "Pattern (.*): ")
-;;                  inferior-ess-objects-pattern))
-;;       (pattern (if (string= pattern "") ".*" pattern))
-;;       (the-command (format inferior-ess-objects-command the-posn pattern))
-;;       (the-message (concat ">>> Position "
-;;                            the-posn
-;;                            " ("
-;;                            (nth (1- the-posn) (ess-search-list))
-;;                            ") (pattern = "
-;;                            pattern
-;;                            ")\n")))
-;;    (ess-execute the-command invert "S objects" the-message)))
-
 (defun ess-execute-search (invert)
   "Send the `inferior-ess-search-list-command' command to the `ess-language' process.
  [search(..) in S]"

lisp/ess-mode.el

@@ -529,16 +529,15 @@ ess-mode."
      (repl "\\(<-\\)?")                 ; replacement (function)
      (Sym-0 "\\(\\sw\\|\\s_\\)")        ; symbol
      (Symb  (concat Sym-0 "+"))
-     (xSymb (concat "\\[?\\[?" Sym-0 "*")); symbol / [ / [[ / [symbol / [[symbol
+     (xSymb "[^ \t\n\"']+") ;; (concat "\\[?\\[?" Sym-0 "*")); symbol / [ / [[ / [symbol / [[symbol
      ;; FIXME: allow '%foo%' but only when quoted; don't allow [_0-9] at beg.
      (_or_  "\\)\\|\\(")                ; OR
      (space "\\(\\s-\\|\n\\)*")         ; white space
 
      (part-1 (concat
               "\\(" ;;--------outer Either-------
               "\\(\\("          ; EITHER
-              ;; Q xSymb repl Sym-0 "*" Q  ; quote ([) (replacement) symbol quote
-              Q "[^ \t\n\"']+" Q ;; any function name between quotes
+              Q xSymb Q         ; any function name between quotes
               _or_
               "\\(^\\|[ ]\\)" Symb      ; (beginning of name) + Symb
               "\\)\\)"))        ; END EITHER OR
@@ -561,6 +560,7 @@ ess-mode."
               space "function\\s-*(" ; whitespace, function keyword, parenthesis
               ))
      )
+
   (defvar ess-R-function-pattern
     (concat part-1
             "\\s-*\\(<-\\|=\\)" ; whitespace, assign

lisp/ess-sas-l.el

@@ -127,6 +127,7 @@ A .lst file is a SAS listing file when:
   (when ess-automatic-sas-log-or-lst-mode
     (let* ((bfn (buffer-file-name))
            (log (and bfn
+                     (string-match-p "\\.lst$" bfn)
                      (replace-regexp-in-string "\\.lst$" ".log" bfn))))
       (and log
            (file-exists-p log)

lisp/ess-site.el

@@ -187,13 +187,14 @@ for ESS, such as icons.")
 
 ;;(1.2) If ess.info is not found, then ess-lisp-directory/../doc/info is added
 ;; resurrecting Stephen's version with a bug-fix & xemacs compatibility
+(if (fboundp 'locate-file) (progn
 (unless (locate-file "ess.info"
                      (if (featurep 'xemacs)
                          Info-directory-list
                        Info-default-directory-list))
   (add-to-list (if (featurep 'xemacs)
                    'Info-directory-list 'Info-default-directory-list)
-               (expand-file-name "../doc/info/" ess-lisp-directory)))
+               (expand-file-name "../doc/info/" ess-lisp-directory)))))
 
 
 ;; ALWAYS: