Merge branch 'trunk'

ChangeLog

@@ -1,3 +1,7 @@
+2014-09-13  ESS Maintainers <[email protected]>
+
+  * Version 14.09 released.
+
 2013-12-10  Rodney Sparapani  <[email protected]>
 
 	* Makeconf (SITELISP): tersely documenting SITELISP

Makeconf

@@ -18,7 +18,7 @@
 ##                 Specify either PREFIX or DESTDIR to over-ride /usr
 DESTDIR=/usr
 PREFIX=$(DESTDIR)
-#
+
 ##__ GNU Emacs __
 EMACS=emacs
 SITELISP=$(PREFIX)/share/emacs/site-lisp
@@ -32,16 +32,14 @@ ETCDIR =$(PREFIX)/share/emacs/etc/ess
 #LISPDIR=$(SITELISP)/ess
 #INFODIR=$(PREFIX)/share/xemacs/site-packages/info
 #ETCDIR =$(PREFIX)/share/xemacs/site-packages/etc/ess
-#
 
 ##__ GNU Emacs __  for Mac OS X with NeXTstep (Cocoa or GNUstep)
 # PREFIX=/Applications/Emacs.app/Contents/Resources
 # EMACS=/Applications/Emacs.app/Contents/MacOS/Emacs
 # SITELISP=$(PREFIX)/site-lisp
 # LISPDIR=$(SITELISP)/ess
-# INFODIR=$(PREFIX)/info
+# INFODIR=/usr/local/info
 # ETCDIR =$(PREFIX)/etc/ess
-#
 
 ##__ Aquamacs __  (donated by Dan Knoepfle, Mar 26, 2011)
 # PREFIX=/Applications/Aquamacs.app/Contents/Resources/lisp/aquamacs/edit-modes
@@ -50,7 +48,6 @@ ETCDIR =$(PREFIX)/share/emacs/etc/ess
 # LISPDIR=$(PREFIX)/ess-mode/lisp
 # INFODIR=/Applications/Aquamacs.app/Contents/Resources/info
 # ETCDIR=$(PREFIX)/ess-mode/etc
-#
 
 ## the following command is the same for recent versions of both Emacs and XEmacs
 EMACSBATCH = $(EMACS) -batch -no-site-file -no-init-file
@@ -68,24 +65,24 @@ EMACSBATCH = $(EMACS) -batch -no-site-file -no-init-file
 ##                 1st) source-file & 2nd) target-directory
 ## UNINSTALL       deletes all arguments
 ## DOCDIR          Destination of other doc files
-#
+
 SHELL = /bin/sh
-#
+
 MAKEINFO = LC_ALL=C LANG=en makeinfo
 # new:  MAKEHTML <output>.html  <input>.texi  {necessary to build 'Index'}
 MAKEHTML = $(MAKEINFO) --html --no-split --css-include=atouchofstyle.css -o
 ##                            ^^^^^^^^^^ today's bandwidth is fast
 #MAKETXT  = $(MAKEINFO) --no-validate --no-headers --no-split -o -
 MAKETXT  = $(MAKEINFO) --no-validate --plaintext --no-split -o -
-#
+
 INSTALLDIR = mkdir -p
 #INSTALLDIR = install -d
-#
+
 INSTALL = cp -p
 #INSTALL = install
-#
+
 UNINSTALL = rm -f
-#
+
 DOCDIR=$(PREFIX)/share/doc/ess
 
 ## Section 3

VERSION

@@ -1 +1 @@
-14.08
+14.09

debian/changelog

@@ -1,3 +1,9 @@
+ess (14.09-1) unstable; urgency=low
+
+  * New upstream version released today 
+
+ -- Dirk Eddelbuettel <[email protected]>  Sat, 13 Sep 2014 09:03:04 -0500
+
 ess (13.09-1-1) unstable; urgency=low
 
   * New upstream version released today 

debian/control

@@ -5,7 +5,7 @@ Maintainer: ESS Debian Maintainers <[email protected]>
 Uploaders: Dirk Eddelbuettel <[email protected]>
 Standards-Version: 3.9.5
 Build-Depends: debhelper (>= 7.0.0)
-Build-Depends-Indep: texlive-base, texlive-latex-base, texlive-latex-recommended, texlive-latex-extra, texlive-generic-recommended, texlive-extra-utils, texinfo, texi2html, autotools-dev
+Build-Depends-Indep: texlive-base, texlive-latex-base, texlive-latex-recommended, texlive-latex-extra, texlive-generic-recommended, texlive-extra-utils, texinfo, autotools-dev
 Homepage: http://ess.r-project.org
 
 Package: ess

doc/ess.texi

@@ -23,7 +23,7 @@ ESS version @ESSVER
 @c @end ifhtml
 @c
 @author Current Documentation by The ESS Developers
-@author Copyright @copyright{} 2002--2013 The ESS Developers
+@author Copyright @copyright{} 2002--2014 The ESS Developers
 @author Copyright @copyright{} 1996--2001 A.J. Rossini
 @author Original Documentation by David M. Smith
 @author Copyright @copyright{} 1992--1995 David M. Smith
@@ -521,7 +521,7 @@ Other ways to setup a remote ESS connection are through @code{ess-remote}.
 @item Start the ESS process on the remote machine, for example with one of
 the commands @samp{Splus}, or @samp{R}, or @samp{sas -stdio}.
 
-@item Start @samp{M-x ess-remote}.  
+@item Start @samp{M-x ess-remote}.
 You will be prompted for a program name with completion.  Choose
 one. Your process is now known to ESS.  All the usual ESS commands
 (@samp{C-c C-n} and its relatives) now work with the S language
@@ -2971,7 +2971,7 @@ something like:
     @code{
        Warning: Class "boo" is defined (with package slot ‘foo’) but no
        metadata object found to revise subclass information---not exported?
-       }      
+       }
 
 You can safely ignore this warnings.
 

doc/newfeat.texi

@@ -1,13 +1,30 @@
 @comment @itemize @w{}
 @comment @item
 
-Changes / Selected Bug Fixes in 14.04:
+Changes / Selected Bug Fixes in 14.09:
 @itemize @bullet
-@item @ESS{[R]}: @code{ess-execute-screen-options} uses correct screen width in terminal sessions
-@item @ESS{[R]}: command cleaning with @kbd{C-u C-u C-y} was broken with lines containing " + "
+@item @ESS{[Julia]}: Executable is changed to @code{julia}.
+@item @ESS{[Julia]}: Completion and help system was adjusted to Julia
+v.0.3.0. Julia v.0.2.x is no more supported.
+@item @ESS{[R]}: Running R with @code{gdb} debugger now works as expected
+@item @iESS{}: Inferior ESS buffers are now derived from @code{comint-mode}
+@item @ESS{[R]}: @code{ess-execute-screen-options} uses correct screen
+width in terminal sessions
+@item @ESS{}: @code{ess-build-tags-for-directory} works when no TAGS file
+name was provided
+@item @ESS{}: @code{ess-continued-statement-offset} is now respected everywhere
+except inside of the @code{if} test condition.
+@item @ESS{}: New variable @code{ess-first-continued-statement-offset} for
+indentation of the first line in multiline statements.
+@item @ESS{R}: Starting @kbd{,} in multiline statements indentation is now
+ignored to achieve a more pleasant alignment.
+@item @ESS{R}: Improved behavior of @kbd{RET} in roxygen blocks.
+@item @ESS{[R]}: command cleaning with @kbd{C-u C-u C-y} was broken with
+lines containing " + "
 @item @ESS{[R]}: fixed "empty watch window bug"
 @item @ESS{[R]}: don't ask for help location on ac-quick-help (request of github #81)
-@item @ESS{[R]}: "importClassesFrom" and "importMethodsFrom" were added to the list of two-parameter roxygen commands 
+@item @ESS{[R]}: "importClassesFrom" and "importMethodsFrom" were added to
+the list of two-parameter roxygen commands
 @item @ESS{[R]}: fix vignetes display and hyperlinks (were broken in 13.09-1)
 @item @ESS{[Julia]}: recognize function names ending with !
 @item @ESS{[Julia]}: fix indentation of "for" comprehension syntax within brackets.
@@ -36,15 +53,15 @@ Leading comments are automatically removed before the evaluation
 @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
-when appropriate.  Indent comments and CARDS statement 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}: 
+@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 
+@item @ESS{}: installation with @code{make install} was simplified and should work
 out of the box on most *nix systems
 @item @ESS{} installation instructions simplified
 @item fixed font-lock bug introduced in 13.09 that was causing very slow process output

ess-autoloads.el

@@ -1,6 +1,7 @@
 ;;; ess-autoloads.el --- Emacs Speaks Statistics: statistical programming within Emacs
 
 ;; Copyright (C) 2012 Donald E. Curtis
+;; Copyright (C) 2014 The ESS Core Team
 
 ;; Original Author: Donald E. Curtis
 ;; Created: March 5, 2012

etc/ESSR/VERSION

@@ -1 +1 @@
-1.1.6
+1.1.7

lisp/ess-custom.el

@@ -132,7 +132,7 @@
   :prefix "ess-")
 ;; Variables (not user-changeable)
 
-(defvar ess-version "14.08" ;; updated by 'make'
+(defvar ess-version "14.09" ;; updated by 'make'
   "Version of ESS currently loaded.")
 
 (defvar ess-revision nil ;; set
@@ -751,7 +751,7 @@ If not number, the statements are indented at open-parenthesis following
         (cons 'ess-arg-function-offset-new-line '(default-value 'ess-arg-function-offset-new-line))
         (cons 'ess-close-brace-offset '(default-value 'ess-close-brace-offset))
         )
-  "Default style constructed from initial values of indentation variables.")
+  "Style constructed from initial (default) values of ESS indentation variables.")
 
 (defvar ess-style-alist
   (cons ess-default-style-list

lisp/ess-inf.el

@@ -96,7 +96,7 @@ If ess-plain-first-buffername, then initial process is number-free."
                         (= n 1))) ; if not both first and plain-first add number
               (concat ":" (number-to-string n)))))
 
-(defun inferior-ess (&optional ess-start-args)
+(defun inferior-ess (&optional ess-start-args customize-alist no-wait)
   "Start inferior ESS process.
 
 Without a prefix argument, starts a new ESS process, or switches
@@ -133,10 +133,12 @@ Alternatively, it can appear in its own frame if
 
   (interactive)
 
-  (let ((temp-ess-dialect (eval (cdr (assoc 'ess-dialect
-                                            ess-customize-alist))))
-        (temp-ess-lang (eval (cdr (assoc 'ess-language
-                                         ess-customize-alist)))))
+  (let* ((ess-customize-alist (or customize-alist
+                                  ess-customize-alist))
+         (temp-ess-dialect (eval (cdr (assoc 'ess-dialect
+                                             ess-customize-alist))))
+         (temp-ess-lang (eval (cdr (assoc 'ess-language
+                                          ess-customize-alist)))))
 
     (run-hooks 'ess-pre-run-hook)
     (ess-write-to-dribble-buffer
@@ -294,8 +296,9 @@ Alternatively, it can appear in its own frame if
             ;; (inferior-ess-wait-for-prompt)
             (inferior-ess-mark-as-busy (get-process procname))
             (process-send-string (get-process procname) "\n") ;; to be sure we catch the prompt if user comp is super-duper fast.
-            (ess-write-to-dribble-buffer "(inferior-ess: waiting for process to start (before hook)\n")
-            (ess-wait-for-process (get-process procname) nil 0.01)
+            (unless no-wait 
+              (ess-write-to-dribble-buffer "(inferior-ess: waiting for process to start (before hook)\n")
+              (ess-wait-for-process (get-process procname) nil 0.01))
 
             ;; arguments cache
             (ess-process-put 'funargs-cache (make-hash-table :test 'equal))
@@ -317,8 +320,9 @@ Alternatively, it can appear in its own frame if
             ;; EXTRAS
             (ess-load-extras t)
             ;; user initialization can take some time ...
-            (ess-write-to-dribble-buffer "(inferior-ess 3): waiting for process after hook")
-            (ess-wait-for-process (get-process procname)))
+            (unless no-wait
+              (ess-write-to-dribble-buffer "(inferior-ess 3): waiting for process after hook")
+              (ess-wait-for-process (get-process procname))))
 
           (with-current-buffer buf
             (rename-buffer buf-name-str t))
@@ -428,26 +432,27 @@ Return the 'busy state."
   (let ((busy (not (string-match (concat "\\(" inferior-ess-primary-prompt "\\)\\'") string))))
     (process-put proc 'busy-end? (and (not busy)
                                       (process-get proc 'busy)))
-    (if (not busy) (process-put proc 'running-async? nil))
+    (when (not busy)
+      (process-put proc 'running-async? nil))
     (process-put proc 'busy busy)
     (process-put proc 'sec-prompt
                  (when inferior-ess-secondary-prompt
                    (string-match (concat "\\(" inferior-ess-secondary-prompt "\\)\\'") string)))
     (unless no-timestamp
       (process-put proc 'last-eval (current-time)))
-    busy
-    ))
+    busy))
 
 (defun inferior-ess-mark-as-busy (proc)
   (process-put proc 'busy t)
   (process-put proc 'sec-prompt nil))
 
 (defun inferior-ess-run-callback (proc string)
-  ;; callback is stored in 'callbacks proc property. It can be either a function
-  ;; to be called with two artuments PROC and STRING or a cons cell of the form
-  ;; (func . suppress) where, if suppress is non-nil next process output will be
-  ;; suppressed.
-  (when (process-get proc 'busy-end?)
+  ;; callback is stored in 'callbacks proc property. Callbacks is a list that
+  ;; can contain either functions to be called with two artuments PROC and
+  ;; STRING, or cons cells of the form (func . suppress). If SUPPRESS is non-nil
+  ;; next process output will be suppressed.
+  (unless (process-get proc 'busy)
+    ;; only one callback is implemented for now
     (let* ((cb (car (process-get proc 'callbacks)))
            (listp (not (functionp cb)))
            (suppress (and listp (consp cb) (cdr cb)))

lisp/ess-r-d.el

@@ -304,7 +304,7 @@ before ess-site is loaded) for it to take effect."))
   process.")
 
 (defun ess--R-load-ESSR ()
-  "Load/INSTALL/Update ESSR"
+  "Load/INSTALL/Update ESSR."
   (let* ((ESSR-directory (expand-file-name "ESSR" ess-etc-directory))
          (src-dir (expand-file-name "R" ESSR-directory)))
 
@@ -351,8 +351,6 @@ Optional prefix (C-u) allows to set command line arguments, such as
 If you have certain command line arguments that should always be passed
 to R, put them in the variable `inferior-R-args'."
   (interactive "P")
-  ;; get settings, notably inferior-R-program-name :
-  (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"
@@ -372,43 +370,57 @@ to R, put them in the variable `inferior-R-args'."
                                    (concat " [other than '" r-always-arg "']"))
                                " ? "))
                     nil)))
+         (cust-alist (copy-alist R-customize-alist))
+         (gdbp (string-match-p "gdb" r-start-args))
          use-dialog-box)
 
+    (when gdbp
+      (setcdr (assoc 'inferior-ess-secondary-prompt cust-alist)
+              (format "\\(%s\\)\\|\\((gdb) \\)"
+                      (cdr (assoc 'inferior-ess-secondary-prompt cust-alist)))))
+
     (when (or ess-microsoft-p
               (eq system-type 'cygwin))
       (setq use-dialog-box nil)
-      (if ess-microsoft-p ;; default-process-coding-system would break UTF locales on Unix
-          (setq default-process-coding-system '(undecided-dos . undecided-dos))))
+      (when ess-microsoft-p ;; default-process-coding-system would break UTF locales on Unix
+        (setq default-process-coding-system '(undecided-dos . undecided-dos))))
 
-    (inferior-ess r-start-args)
+    (inferior-ess r-start-args cust-alist gdbp)
 
     (ess-process-put 'funargs-pre-cache ess-R--funargs-pre-cache)
+    ;; We need to use callback, because R might start with a gdb process
+    (ess-process-put 'callbacks '(R-initialize-on-start))
+    ;; trigger the callback
+    (process-send-string (get-process ess-local-process-name) "\n")
 
     (remove-hook 'completion-at-point-functions 'ess-filename-completion 'local) ;; should be first
     (add-hook 'completion-at-point-functions 'ess-R-object-completion nil 'local)
     (add-hook 'completion-at-point-functions 'ess-filename-completion nil 'local)
-
-    ;;-------------------------
     (setq comint-input-sender 'inferior-R-input-sender)
+
     (ess-write-to-dribble-buffer
      (format "(R): inferior-ess-language-start=%s\n"
-             inferior-ess-language-start))
+             inferior-ess-language-start))))
 
-    (when ess-can-eval-in-background
-      (ess-async-command-delayed
-       "invisible(installed.packages())\n" nil (get-process ess-local-process-name)
-       ;; "invisible(Sys.sleep(10))\n" nil (get-process ess-local-process-name) ;; test only
-       (lambda (proc) (process-put proc 'packages-cached? t))))
+(defun R-initialize-on-start (&optional proc string)
+  "This function is run after the first R prompt.
+Executed in process buffer."
+  (interactive)
 
-    (ess--R-load-ESSR)
+  (when ess-can-eval-in-background
+    (ess-async-command-delayed
+     "invisible(installed.packages())\n" nil (get-process ess-local-process-name)
+     ;; "invisible(Sys.sleep(10))\n" nil (get-process ess-local-process-name) ;; test only
+     (lambda (proc) (process-put proc 'packages-cached? t))))
 
-    (if inferior-ess-language-start
-        (ess-eval-linewise inferior-ess-language-start
-                           nil nil nil 'wait-prompt))
+  (ess--R-load-ESSR)
 
-    (with-ess-process-buffer nil
-      (run-mode-hooks 'ess-R-post-run-hook))))
+  (when inferior-ess-language-start
+    (ess-eval-linewise inferior-ess-language-start
+                       nil nil nil 'wait-prompt))
 
+  (with-ess-process-buffer nil
+    (run-mode-hooks 'ess-R-post-run-hook)))
 
 
 ;; (defun ess--R-cache-installed-packages ()