#+TITLE: .emacs file 
#+OPTIONS: toc:nil num:nil ^:nil

* General settings
** Save desktop
#+begin_src emacs-lisp
(desktop-save-mode 1)
#+end_src
** COMMENT Autosave desktop every hour
#+begin_src emacs-lisps
  (run-at-time "00:59" 3600 'org-save-all-org-buffers)
#+end_src
** Search path definitions
#+begin_src emacs-lisp
  (add-to-list 'load-path "~/.emacs.d/site-lisp")
#+end_src
* COMMENT CEDET
  See cedet/common/cedet.info for configuration details.
#+begin_src emacs-lisps
   (add-to-list 'load-path "~/.emacs.d/cedet")
   (load-file "~/.emacs.d/cedet/common/cedet.el")
#+end_src
  Optional other options
#+begin_src emacs-lisps
  ;; Enable EDE (Project Management) features
  (global-ede-mode 1)

  ;; Enable EDE for a pre-existing C++ project
  ;; (ede-cpp-root-project "NAME" :file "~/myproject/Makefile")


  ;; Enabling Semantic (code-parsing, smart completion) features
  ;; Select one of the following:

  ;; * This enables the database and idle reparse engines
  ; (semantic-load-enable-minimum-features)

  ;; * This enables some tools useful for coding, such as summary mode
  ;;   imenu support, and the semantic navigator
  ; (semantic-load-enable-code-helpers)

  ;; * This enables even more coding tools such as intellisense mode
  ;;   decoration mode, and stickyfunc mode (plus regular code helpers)
  ;; (semantic-load-enable-gaudy-code-helpers)

  ;; * This enables the use of Exuberent ctags if you have it installed.
  ;;   If you use C++ templates or boost, you should NOT enable it.
  ;; (semantic-load-enable-all-exuberent-ctags-support)

  ;; Enable SRecode (Template management) minor-mode.
  (global-srecode-minor-mode 1)
#+end_src
* COMMENT Ecb 
#+begin_src emacs-lisps
  (add-to-list 'load-path "~/.emacs.d/ecb")
  (require 'ecb-autoloads)
  (setq ecb-layout-name "left3")
  (setq ecb-layout-window-sizes (quote (("left8" (0.23076923076923078 . 0.23333333333333334) (0.23076923076923078 . 0.25) (0.23076923076923078 . 0.2833333333333333) (0.23076923076923078 . 0.21666666666666667)) ("left3" (0.22162162162162163 . 0.10344827586206896) (0.22162162162162163 . 0.46551724137931033) (0.22162162162162163 . 0.41379310344827586)))))
  (setq ecb-options-version "2.32")
  (setq ecb-toggle-layout-sequence (quote ("left9" "left14" "left3")))
#+end_src
* ESS
** Load ess
#+begin_src emacs-lisp
  (add-to-list 'load-path "~/.emacs.d/ess")
  (load "~/.emacs.d/ess/lisp/ess-site")
  (require 'ess-site)
  (font-lock-add-keywords 'ess-mode
#+end_src
** Add highlighting for certain keywords
#+begin_src emacs-lisp
   '(("\\<\\(FIXME\\|TODO\\|COMMENT\\|DONE\\|CHANGES\\|FIXED\\)\\>" 1 font-lock-warning-face prepend)))
#+end_src
** Further customisations
#+begin_src emacs-lisp
   (setq inferior-R-args "--vanilla")
   (setq ess-eval-visibly-p nil)
   (setq inferior-ess-same-window t)
   (setq inferior-ess-client-command "Initial")
   (setq inferior-ess-own-frame nil)
   (setq ess-ask-for-ess-directory nil)
#+end_src
** Make html help in R default
#+begin_src emacs-lisp
 (setq inferior-ess-r-help-command "help(\"%s\", help_type=\"html\")\n")
#+end_src
** r-utils
#+begin_src emacs-lisp
   (require 'r-utils)
#+end_src
** R-object tooltips
based on [[http://blogisticreflections.wordpress.com/2009/10/01/r-object-tooltips-in-ess/]]
Here are the comments as on the website:
;; ess-R-object-tooltip.el
;; 
;; I have defined a function, ess-R-object-tooltip, that when
;; invoked, will return a tooltip with some information about
;; the object at point.  The information returned is
;; determined by which R function is called.  This is controlled
;; by an alist, called ess-R-object-tooltip-alist.  The default is
;; given below.  The keys are the classes of R object that will
;; use the associated function.  For example, when the function
;; is called while point is on a factor object, a table of that
;; factor will be shown in the tooltip.  The objects must of course
;; exist in the associated inferior R process for this to work.
;; The special key "other" in the alist defines which function
;; to call when the class is not mached in the alist.  By default,
;; the str function is called, which is actually a fairly useful
;; default for data.frame and function objects.
;; 
;; The last line of this file shows my default keybinding.
;; I simply save this file in a directory in my load-path
;; and then place (require 'ess-R-object-tooltip) in my .emacs
#+begin_src emacs-lisp
  ;; the alist
  (setq ess-R-object-tooltip-alist
        '((numeric    . "summary")
          (factor     . "table")
          (integer    . "summary")
          (lm         . "summary")
          (other      . "str")))
  
  (defun ess-R-object-tooltip ()
    "Get info for object at point, and display it in a tooltip."
    (interactive)
    (let ((objname (current-word))
          (curbuf (current-buffer))
          (tmpbuf (get-buffer-create "**ess-R-object-tooltip**")))
      (if objname
          (progn
            (ess-command (concat "class(" objname ")\n")  tmpbuf )
            (set-buffer tmpbuf)
            (let ((bs (buffer-string)))
              (if (not(string-match "\(object .* not found\)\|unexpected" bs))
                  (let* ((objcls (buffer-substring
                                  (+ 2 (string-match "\".*\"" bs))
                                  (- (point-max) 2)))
                         (myfun (cdr(assoc-string objcls
                                                  ess-R-object-tooltip-alist))))
                    (progn
                      (if (eq myfun nil)
                          (setq myfun
                                (cdr(assoc-string "other"
                                                  ess-R-object-tooltip-alist))))
                      (ess-command (concat myfun "(" objname ")\n") tmpbuf)
                      (let ((bs (buffer-string)))
                        (progn
                          (set-buffer curbuf)
                          (tooltip-show-at-point bs 0 30)))))))))
      (kill-buffer tmpbuf)))
  
  ;; key map for R files and inferior mode
  (define-key ess-mode-map "\C-c\C-g" 'ess-R-object-tooltip)
  (define-key inferior-ess-mode-map "\C-c\C-g" 'ess-R-object-tooltip)
  
  (provide 'ess-R-object-tooltip)
#+end_src
** Shift Enter
>From [[http://www.emacswiki.org/emacs/ESSShiftEnter]]
- if R if not running, it starts automatically and opens an inferior frame
- if the region is active, evaluates the region
- otherwise, it runs the current line
#+begin_src emacs-lisps
  (setq ess-ask-for-ess-directory nil)
  (setq ess-local-process-name "R")
  (setq ansi-color-for-comint-mode 'filter)
  (setq comint-prompt-read-only t)
  (setq comint-scroll-to-bottom-on-input t)
  (setq comint-scroll-to-bottom-on-output t)
  (setq comint-move-point-for-output t)
  (defun my-ess-start-R ()
    (interactive)
    (if (not (member "*R*" (mapcar (function buffer-name) (buffer-list))))
      (progn
	(delete-other-windows)
	(setq w1 (selected-window))
	(setq w1name (buffer-name))
	(setq w2 (split-window w1))
	(R)
	(set-window-buffer w2 "*R*")
	(set-window-buffer w1 w1name))))
  (defun my-ess-eval ()
    (interactive)
    (my-ess-start-R)
    (if (and transient-mark-mode mark-active)
	(call-interactively 'ess-eval-region)
      (call-interactively 'ess-eval-line-and-step)))
  (add-hook 'ess-mode-hook
	    '(lambda()
	       (local-set-key [(shift return)] 'my-ess-eval)))
  (add-hook 'inferior-ess-mode-hook
	    '(lambda()
	       (local-set-key [C-up] 'comint-previous-input)
	       (local-set-key [C-down] 'comint-next-input)))
  (require 'ess-site)
#+end_src
** hideshow
  hideshow-org (http://github.com/secelis/hideshow-org/tree/master)
#+begin_src emacs-lisp
  (require 'hideshow)
  (require 'hideshow-org)
  (add-to-list 'hs-special-modes-alist
               '(ess-mode "{" "}" "/[*/]" nil
                          hs-c-like-adjust-block-beginning))
  (global-set-key "\C-ch" 'hs-org/minor-mode) ;; toggles hideshow-org
  ;; (add-hook 'ess-mode-hook 'hs-org/minor-mode) ;; starts for ESS files
  (add-hook 'ess-mode-hook '(lambda () (hs-org/minor-mode 1)))
#+end_src
** Additional syntax highlighting
#+begin_src emacs-lisp
  (add-hook 'ess-mode-hook
            '(lambda()
               (font-lock-add-keywords nil
                                       '(("\\<\\(if\\|for\\|function\\|return\\)\\>[\n[:blank:]]*(" 1
                                          font-lock-keyword-face) ; must go first to override highlighting below
                                         ("\\<\\([.A-Za-z][._A-Za-z0-9]*\\)[\n[:blank:]]*(" 1
                                          font-lock-function-name-face) ; highlight function names
                                         ("\\([(,]\\|[\n[:blank:]]*\\)\\([.A-Za-z][._A-Za-z0-9]*\\)[\n[:blank:]]*=[^=]" 2
                                          font-lock-reference-face) ;highlight argument names
                                         ))
               ))
#+end_src
** hideshow for ESS
#+begin_src emacs-lisp
  (autoload 'hideshowvis-enable "hideshowvis" "Highlight foldable regions")
  (dolist (hook (list 'emacs-lisp-mode-hook
  'ess-mode-hook))
  (add-hook hook 'hideshowvis-enable))
  (setq hs-special-modes-alist
  (cons '(ess-mode "{" "}" "#" nil nil) hs-special-modes-alist))

  (define-fringe-bitmap 'hs-marker [0 24 24 126 126 24 24 0])

  (defcustom hs-fringe-face 'hs-fringe-face
  "*Specify face used to highlight the fringe on hidden regions."
  :type 'face
  :group 'hideshow)

  (defface hs-fringe-face
  '((t (:foreground "#888" :box (:line-width 2 :color "grey75" :style released-button))))
  "Face used to highlight the fringe on folded regions"
  :group 'hideshow)

  (defcustom hs-face 'hs-face
  "*Specify the face to to use for the hidden region indicator"
  :type 'face
  :group 'hideshow)

  (defface hs-face
  '((t (:background "#ff8" :box t)))
  "Face to hightlight the ... area of hidden regions"
  :group 'hideshow)

  (defun display-code-line-counts (ov)
  (when (eq 'code (overlay-get ov 'hs))
  (let* ((marker-string "*fringe-dummy*")
  (marker-length (length marker-string))
  (display-string (format "(%d)..." (count-lines (overlay-start ov) (overlay-end ov))))
  )
  (overlay-put ov 'help-echo "Hiddent text. C-c,= to show")
  (put-text-property 0 marker-length 'display (list 'left-fringe 'hs-marker 'hs-fringe-face) marker-string)
  (overlay-put ov 'before-string marker-string)
  (put-text-property 0 (length display-string) 'face 'hs-face display-string)
  (overlay-put ov 'display display-string)
  )))

  (setq hs-set-up-overlay 'display-code-line-counts)
#+end_src

** COMMENT TODO Syntax highlighting for functions in R NOT WORKINg
  based on https://mail.google.com/mail/#label/Lists%2FESS/125131ed24688970
  The following code needs to be run in R:
  
  obj <- do.call("c", sapply(c("package:base", "package:stats",
  "package:utils"), objects, all.names=TRUE))
  re <- "(^[^.[:alpha:][:digit:]]|<-|__)"  # to remove "weird" functions
  obj <- obj[-grep(re, obj)]
  fpath <- file.path(Sys.getenv("HOME"), ".emacs.d", "R-function-names.txt")
  write.table(obj, fpath, quote=FALSE, row.names=FALSE, col.names=FALSE)
  
  Read a whole file into list of lines
  Author: Xah Lee
  see http://xahlee.org/emacs/elisp_process_lines.html
#+begin_src emacs-lisps
  (defun read-lines (file)
  "Return a list of lines in FILE."
  (with-temp-buffer
  (insert-file-contents file)
  (split-string
  (buffer-string) "\n" t)
  )
  )

  (add-hook 'ess-mode-hook
  '(lambda()
  (setq ess-my-extra-R-function-keywords
  (read-lines "~/.emacs.d/R-function-names.txt"))
  (setq ess-R-mode-font-lock-keywords
  (append ess-R-mode-font-lock-keywords
  (list (cons (concat "\\<" (regexp-opt
  ess-my-extra-R-function-keywords 'enc-paren) "\\>")
  'font-lock-function-name-face))))))
#+end_src
* COMMENT Graphviz
Load graphviz-dot-mode
#+begin_src emacs-lisps
  (load-file "~/emacs/graphviz-dot-mode.el") 
  (setq graphviz-dot-view-command "display %s")
#+end_src
* SSH Major mode
#+begin_src emacs-lisp
  (load-file "/home/rkrug/.emacs.d/site-lisp/ssh.el") 
#+end_src
* COMMENT Bookmark (bm)
#+begin_src emacs-lisps
  (setq bm-restore-repository-on-load t)
  (require 'bm)
  (global-set-key (kbd "<f2>") 'bm-toggle)
  (global-set-key (kbd "<C-f2>")   'bm-next)
  (global-set-key (kbd "<s-f2>") 'bm-previous)
  
  ;; make bookmarks persistent as default
  (setq-default bm-buffer-persistence t)
  
  ;; Loading the repository from file when on start up.
  (add-hook' after-init-hook 'bm-repository-load)
  
  ;; Restoring bookmarks when on file find.
  (add-hook 'find-file-hooks 'bm-buffer-restore)
  
  ;; Saving bookmark data on killing a buffer
  (add-hook 'kill-buffer-hook 'bm-buffer-save)
  
  ;; Saving the repository to file when on exit.
  ;; kill-buffer-hook is not called when emacs is killed, so we
  ;; must save all bookmarks first.
  (add-hook 'kill-emacs-hook '(lambda nil
                                (bm-buffer-save-all)
                                (bm-repository-save)))
#+end_src
* COMMENT anything
#+begin_src emacs-lisp
  (require 'anything)
  (require 'anything-config)
  (require 'recentf)

  (global-set-key [f11] 'anything)
  (remove-hook 'kill-emacs-hook 'anything-c-adaptive-save-history)
#+end_src
** R objects
#+begin_src emacs-lisps
  (setq anything-c-source-R-help
  '((name . "R objects / help")
  (init . (lambda ()
  ; this grabs the process name associated with the buffer
  (setq anything-c-ess-local-process-name ess-local-process-name)))
  (candidates . (lambda ()
  (condition-case nil
  (ess-get-object-list anything-c-ess-local-process-name)
  (error nil))))
  (action
  ("help" . ess-display-help-on-object)
  ("head (10)" . (lambda(obj-name)
  (ess-execute (concat "head(" obj-name ", n = 10)\n") nil (concat "R head: " obj-name))))
  ("head (100)" . (lambda(obj-name)
  (ess-execute (concat "head(" obj-name ", n = 100)\n") nil (concat "R head: " obj-name))))
  ("tail" . (lambda(obj-name)
  (ess-execute (concat "tail(" obj-name ", n = 10)\n") nil (concat "R tail: " obj-name))))
  ("str" . (lambda(obj-name)
  (ess-execute (concat "str(" obj-name ")\n") nil (concat "R str: " obj-name))))
  ("summary" . (lambda(obj-name)
  (ess-execute (concat "summary(" obj-name ")\n") nil (concat "R summary: " obj-name))))
  ("view source" . (lambda(obj-name)
  (ess-execute (concat "print(" obj-name ")\n") nil (concat "R object: " obj-name))))
  ("dput" . (lambda(obj-name)
  (ess-execute (concat "dput(" obj-name ")\n") nil (concat "R dput: " obj-name)))))
  (volatile)))
#+end_src
** R local objects
#+begin_src emacs-lisps
  (setq anything-c-source-R-local
  '((name . "R local objects")
  (init . (lambda ()
  ; this grabs the process name associated with the buffer
  (setq anything-c-ess-local-process-name ess-local-process-name)
  ; this grabs the buffer for later use
  (setq anything-c-ess-buffer (current-buffer))))
  (candidates . (lambda ()
  (let (buf)
  (condition-case nil
  (with-temp-buffer
  (progn
  (setq buf (current-buffer))
  (with-current-buffer anything-c-ess-buffer
  (ess-command "print(ls.str(), max.level=0)\n" buf))
  (split-string (buffer-string) "\n" t)))
  (error nil)))))
  (display-to-real . (lambda (obj-name) (car (split-string obj-name " : " t))))
  (action
  ("str" . (lambda(obj-name)
  (ess-execute (concat "str(" obj-name ")\n") nil (concat "R str: " obj-name))))
  ("summary" . (lambda(obj-name)
  (ess-execute (concat "summary(" obj-name ")\n") nil (concat "R summary: " obj-name))))
  ("head (10)" . (lambda(obj-name)
  (ess-execute (concat "head(" obj-name ", n = 10)\n") nil (concat "R head: " obj-name))))
  ("head (100)" . (lambda(obj-name)
  (ess-execute (concat "head(" obj-name ", n = 100)\n") nil (concat "R head: " obj-name))))
  ("tail" . (lambda(obj-name)
  (ess-execute (concat "tail(" obj-name ", n = 10)\n") nil (concat "R tail: " obj-name))))
  ("print" . (lambda(obj-name)
  (ess-execute (concat "print(" obj-name ")\n") nil (concat "R object: " obj-name))))
  ("dput" . (lambda(obj-name)
  (ess-execute (concat "dput(" obj-name ")\n") nil (concat "R dput: " obj-name)))))
  (volatile)))
#+end_src
** Occur
#+begin_src emacs-lisps
  (setq anything-c-source-occur
  '((name . "Occur")
  (init . (lambda ()
  (setq anything-occur-current-buffer
  (current-buffer))))
  (candidates . (lambda ()
  (let ((anything-occur-buffer (get-buffer-create "*Anything Occur*")))
  (with-current-buffer anything-occur-buffer
  (occur-mode)
  (erase-buffer)
  (let ((count (occur-engine anything-pattern
  (list anything-occur-current-buffer) anything-occur-buffer
  list-matching-lines-default-context-lines case-fold-search
  list-matching-lines-buffer-name-face
  nil list-matching-lines-face
  (not (eq occur-excluded-properties t)))))
  (when (> count 0)
  (setq next-error-last-buffer anything-occur-buffer)
  (cdr (split-string (buffer-string) "\n" t))))))))
  (action . (("Goto line" . (lambda (candidate)
  (with-current-buffer "*Anything Occur*"
  (search-forward candidate))
  (goto-line (string-to-number candidate) anything-occur-current-buffer)))))
  (requires-pattern . 3)
  (volatile)
  (delayed)))
#+end_src
** imenu --- probably ---
#+begin_src emacs-lisps
  (defvar anything-c-imenu-delimiter "/")
  (defvar anything-c-cached-imenu-alist nil)
  (defvar anything-c-cached-imenu-candidates nil)
  (defvar anything-c-cached-imenu-tick nil)
  (make-variable-buffer-local 'anything-c-cached-imenu-alist)
  (make-variable-buffer-local 'anything-c-cached-imenu-candidates)
  (make-variable-buffer-local 'anything-c-cached-imenu-tick)
  (setq anything-c-source-imenu
  '((name . "Imenu")
  (init . (lambda ()
  (setq anything-c-imenu-current-buffer
  (current-buffer))))
  (candidates
  . (lambda ()
  (with-current-buffer anything-c-imenu-current-buffer
  (let ((tick (buffer-modified-tick)))
  (if (eq anything-c-cached-imenu-tick tick)
  anything-c-cached-imenu-candidates
  (setq anything-c-cached-imenu-tick tick
  anything-c-cached-imenu-candidates
  (condition-case nil
  (mapcan
  (lambda (entry)
  (if (listp (cdr entry))
  (mapcar (lambda (sub)
  (concat (car entry) anything-c-imenu-delimiter (car sub)))
  (cdr entry))
  (list (car entry))))
  (setq anything-c-cached-imenu-alist (imenu--make-index-alist)))
  (error nil))))))))
  (volatile)
  (action
  . (lambda (entry)
  (let* ((pair (split-string entry anything-c-imenu-delimiter))
  (first (car pair))
  (second (cadr pair)))
  (imenu
  (if second
  (assoc second (cdr (assoc first anything-c-cached-imenu-alist)))
  (assoc entry anything-c-cached-imenu-alist))))))))
#+end_src
** Visible bookmarks
#+begin_src emacs-lisps
  ;; (defvar anything-c-source-bm
  ;;   '((name . "Visible Bookmarks")
  ;;     (init . (lambda ()
  ;;               (let ((bookmarks (bm-lists)))
  ;;                 (setq anything-bm-marks
  ;;                       (delq nil
  ;;                             (mapcar (lambda (bm)
  ;;                                       (let ((start (overlay-start bm))
  ;;                                             (end (overlay-end bm)))
  ;;                                         (if (< (- end start) 2)
  ;;                                             nil
  ;;                                           (format "%7d: %s"
  ;;                                                   (line-number-at-pos start)
  ;;                                                   (buffer-substring start (1- end))))))
  ;;                                     (append (car bookmarks) (cdr bookmarks))))))))
  ;;     (candidates . (lambda ()
  ;;                     anything-bm-marks))
  ;;     (action . (("Goto line" . (lambda (candidate)
  ;;                                 (goto-line (string-to-number candidate))))))))
#+end_src
** I don't know
#+begin_src emacs-lisps
  ;;
  (setq anything-sources
  (list 
  anything-c-source-buffers ; buffers
  ;;        anything-c-source-bm
  anything-c-source-imenu   ; e.g. Imenu-S menu
  ;;        anything-c-source-recentf ; recent files: needs (require 'recentf)
  anything-c-source-R-local
  anything-c-source-R-help
  anything-c-source-files-in-current-dir
  anything-c-source-occur
  anything-c-source-locate  ; needs the utility locate
  ))
#+end_src
* COMMENT icicles
#+begin_src emacs-lisps
  (load "~/.emacs.d/site-lisp/icicles-install")
  (add-to-list 'load-path "~/.emacs.d/icicles")
  ;; (require 'icicles)
#+end_src
* highlight-parentheses
  http://nschum.de/src/emacs/highlight-parentheses/highlight-parentheses.el
  highlight parenthesis with different colours
#+begin_src emacs-lisp
  (require 'highlight-parentheses)
  (setq hl-paren-colors '("gold" "IndianRed" "cyan" "green" "orange"
  "magenta"))
  (defun hpm-on ()
  (highlight-parentheses-mode t))
  (add-hook 'ess-mode-hook 'hpm-on)
  (add-hook 'inferior-ess-mode-hook 'hpm-on)
#+end_src

* automatically closing brackets
  following from Marc Schwartz from ESS list, works globally
  insert closing bracets automatically
#+begin_src emacs-lisp
  (setq skeleton-pair t)
  ;(setq skeleton-pair-on-word t)
   (global-set-key (kbd "(") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "[") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "{") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "\"") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "\'") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "\`") 'skeleton-pair-insert-maybe)
   (global-set-key (kbd "<") 'skeleton-pair-insert-maybe)
  ;; Delete empty pairs like '()' taken from
  ;; [[http://www.emacswiki.org/cgi-bin/wiki/SkeletonMode#toc14]] ##Deletion section
  (defvar skeletons-alist
  '((?\( . ?\))
  (?\' . ?\')
  (?\" . ?\")
  (?[  . ?])
  (?{  . ?})
  (?<  . ?>)
  (?$  . ?$)))
  (defadvice delete-backward-char (before delete-empty-pair activate)
  (if (eq (cdr (assq (char-before) skeletons-alist)) (char-after))
  (and (char-after) (delete-char 1))))
#+end_src

* load color-theme-hober
  load color-theme package
#+begin_src emacs-lisp
  (add-to-list 'load-path "~/.emacs.d/color-theme")
  (require 'color-theme)
  (eval-after-load "color-theme"
    '(progn
       (color-theme-initialize)
       (color-theme-hober)))
#+end_src

* org-mode
** Basic org mode
*** Initialise org-mode
  http://orgmode.org/manual/Installation.html#Installation
  http://orgmode.org/manual/Activation.html#Activation 
#+begin_src emacs-lisp
  ;; The following lines are always needed.  Choose your own keys.
  (add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
  (global-set-key "\C-cl" 'org-store-link)
  (global-set-key "\C-ca" 'org-agenda)
  (global-set-key "\C-cb" 'org-iswitchb)
  ;; activate font-lock-mode
  (global-font-lock-mode 1)                     ; for all buffers
  ;; (add-hook 'org-mode-hook 'turn-on-font-lock)  ; Org buffers only
  (transient-mark-mode 1)
#+end_src

*** Startup settings
**** Hide leading stars
#+begin_src emacs-lisp
  (setq org-hide-leading-stars t)
#+end_src
**** Indent by default
#+begin_src emacs-lisp
(setq org-startup-indented t)
#+end_src
**** Start with hidden source blocks
#+begin_src emacs-lisp
(setq org-hide-block-startup nil)
#+end_src

*** Use the info files from the actual org-mode used
#+begin_src emacs-lisp
  (add-to-list 'Info-default-directory-list "~/.emacs.d/org-mode/doc/")
#+end_src

** org-capture
  Set the keyboard shortcut and define the templates
#+begin_src emacs-lisp
  (define-key global-map "\C-cc" 'org-capture) 
  (setq org-capture-templates
        '(quote 
           (
            ("t" "Todo" entry (file+headline "~/Documents/orgfiles//notes.org" "Tasks") "* TODO %U %?%i %a") 
            ("j" "Journal" entry (file+headline "~/Documents/orgfiles//notes.org" "") "* %U %? %i %a")
            ("i" "Idea" entry (file+headline "~/Documents/orgfiles//notes.org" "New Ideas") "* %^{Title} %i %a") 
            ("r" "Reference Material" entry (file+headline "reference.org" "") "*%? %&%^g"))
           ))
#+end_src

** org-babel
*** Disable prompting for code execution
#+begin_src emacs-lisp
(setq org-confirm-babel-evaluate nil)
#+end_src
*** Load library-of-babel.el
Load the source-code blocks defined in an Org-mode file into the global "org-babel-library-of-babel" variable
#+begin_src emacs-lisp
(org-babel-lob-ingest "~/.emacs.d/org-mode/contrib/babel/library-of-babel.org")
#+end_src
*** Tangle with comments
#+begin_src emacs-lisp
(setq org-babel-tangle-w-comments t)
;; (add-to-list 'org-babel-default-header-args:R '(:comments . "yes"))
#+end_src
*** sh
**** set shebang for sh script to "#!/bin/bash"
#+begin_src emacs-lisp
;; ensure this variable is defined
(unless (boundp 'org-babel-default-header-args:sh)
(setq org-babel-default-header-args:sh '()))

;; add a default shebang header argument
(add-to-list 'org-babel-default-header-args:sh
'(:shebang . "#!/bin/bash"))
#+end_src
**** Enable language execution
#+begin_src emacs-lisp
(require 'ob-sh)         ;; requires R and ess-mode
#+end_src
*** R
Enable language execution
#+begin_src emacs-lisp
(require 'ob-R)         ;; requires R and ess-mode
#+end_src
*** plantuml
Further info can be find at http://eschulte.github.com/babel-dev/DONE-integrate-plantuml-support.html http://plantuml.sourceforge.net/
Enable language execution
#+begin_src emacs-lisp
(require 'ob-plantuml)         ;; requires R and ess-mode
#+end_src
Set location where plantuml.jar is located
#+begin_src emacs-lisp
(setq org-plantuml-jar-path
      (expand-file-name "~/.emacs.d/org-mode/contrib/scripts/plantuml.jar"))
#+end_src

*** LaTeX
Settings copied from http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-LaTeX.php
**** Activate LaTeX Evaluation
#+begin_src emacs-lisp
(require 'ob-latex)
#+end_src
**** AucTeX
Strongly recommended for editing .tex files. Add the following line to .emacs: 
#+begin_src emacs-lisp
(add-to-list 'load-path "~/.emacs.d/auctex")
(load "auctex.el" nil t t)
#+end_src
*** Raise Noweb-type Errors
Add LaTeX to a list of languages that raise noweb-type errors
Edit the following example to include the languages you use in Org-babel
#+begin_src emacs-lisp
(setq org-babel-noweb-error-langs '("R" "latex"))
#+end_src

*** Set post-tangle-hook for R
This is an example on how to set the hook for loading R files via ess-load-file after tangling. This code should be copied into the .org file, to enable per-file setting of the hook.
#+begin_src emacs-lisp :results silent :tangle no
  ;; (add-hook 'org-babel-post-tangle-hook
  ;;           (lambda () (ess-load-file (buffer-file-name))))
#+end_src
*** Enable fontified LaTeX listing exports. 
Set org-export-latex-listings to a non-nil value and make sure that the packages listings and color are loaded into LaTeX
#+begin_src emacs-lisp
(setq org-export-latex-listings t)
(require 'org-latex)
(add-to-list 'org-export-latex-packages-alist '("" "listings"))
(add-to-list 'org-export-latex-packages-alist '("" "color"))
#+end_src

*** org-babel-tangle-jump-to-org
#+begin_src emacs-lisp
(defun org-babel-tangle-jump-to-org ()
"Jump from a tangled code file to the related Org-mode file."
(interactive)
(let ((mid (point))
target-buffer target-char
start end link path block-name)
(save-window-excursion
(save-excursion
(unless (and (re-search-backward org-bracket-link-analytic-regexp nil t)
(setq start (point))
(setq link (match-string 0))
(setq path (match-string 3))
(setq block-name (match-string 5))
(re-search-forward (concat " " (regexp-quote block-name)
" ends here[\n\r]") nil t)
(setq end (point))
(< start mid) (< mid end))
(error "not in tangled code")))
(when (string-match "::" path)
(setq path (substring path 0 (match-beginning 0))))
(find-file path) (setq target-buffer (current-buffer))
(goto-char start) (org-open-link-from-string link)
(if (string-match "[^ \t\n\r]:\\([[:digit:]]+\\)" block-name)
(org-babel-next-src-block
(string-to-int (match-string 1 block-name)))
(org-babel-goto-named-src-block block-name))
(setq target-char (point)))
(pop-to-buffer target-buffer)
(goto-char target-char)))
#+end_src
** COMMENT Org-mobile settinge --- disabled
#+begin_src emacs-lisps
  (setq org-mobile-directory "/scpc:address@hidden:org/")
#+end_src