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From: Sanjib Sikder <sanjibju2002@gmail.com>
To: emacs-orgmode@gnu.org
Subject: Fwd: Citation in org mode does not compile
Date: Wed, 26 Sep 2012 22:30:42 +0530	[thread overview]
Message-ID: <CAL1SgUpuJYLf4zvUUPSvWKV4r4z-yjoH2gc+hQL_=CZ=Vgmrrg@mail.gmail.com> (raw)
In-Reply-To: <CAL1SgUp87tichwJhr25VpnVTwniH+ivvoxoaiL_9oqFR-Ugcgg@mail.gmail.com>

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I tried the whole day trying the instructions through out various web pages
to have references in scientific document without any success.

C-c C-e p produces the pdf file with question mark in place of reference.

I have attached four files.

BibAbb1.bib is my bibliography file
DOTemacs is the .emacs file
TestSciDocu.org is the org file for scientific writing
TestSciDocu.pdf is the output

Please help me in geeting the citation correctly :(

I am using emacs-snapshot on Ubuntu 12.04.


*Sanjib Sikder
*Ph.D. Fellow
Chemical Engineering
IIT Bombay*


[-- Attachment #1.2: Type: text/html, Size: 933 bytes --]

[-- Attachment #2: BibAbb1.bib --]
[-- Type: application/octet-stream, Size: 810 bytes --]

  author = {PA Ashu and JH Jefferson and AG Cullis and WE Hagston and CR Whitehouse},
  title = {Molecular dynamics simulation of (100) InGaAs/GaAs strained-layer
	relaxation processes},
  journal = {J. Cryst. Growth},
  year = {1995},
  volume = {150},
  pages = {176--179},
  owner = {ss},
  publisher = {Elsevier},
  timestamp = {2011.06.16}

  author = {Brush, S. G.},
  title = {History of the Lenz-Ising model},
  journal = {Rev. Mod. Phys.},
  year = {1967},
  volume = {39},
  pages = {883--893},
  number = {4},
  month = {Oct},
  doi = {10.1103/RevModPhys.39.883},
  file = {brush1967_History of Lenz-Ising Model.pdf:Papers/Ising Model/brush1967_History of Lenz-Ising Model.pdf:PDF},
  numpages = {10},
  publisher = {American Physical Society}

[-- Attachment #3: DOTemacs --]
[-- Type: application/octet-stream, Size: 6102 bytes --]

(global-visual-line-mode 1)

;;;========================Inhibit start-up window ===========================================
(setq inhibit-startup-message t)
;;Following lines will get shown on start up
;; This buffer is for notes you don't want to save, and for Lisp evaluation.
;; If you want to create a file, visit that file with C-x C-f,
;; then enter the text in that file's own buffer.

;;;========================enable syntax highlighting=================================================
;;;different colour to different types of text like comments, maths etc
(global-font-lock-mode t)
;;;highlights marked regions
(setq transient-mark-mode t)
;;;font lock, word wrap, truncate lines, fyspell...........
(add-hook 'org-mode-hook
    (lambda ()
      (setq word-wrap 1)
      (setq truncate-lines nil)
      (flyspell-mode 1)))

(add-to-list 'load-path "~/.emacs.d/predictive")
(add-to-list 'load-path "~/.emacs.d/predictive/texinfo")
(add-to-list 'load-path "~/.emacs.d/predictive/latex")
(add-to-list 'load-path "~/.emacs.d/predictive/html")
(require 'predictive)

;;;Recent files menu in emacs
(require 'recentf)
(recentf-mode 1)
;;;========================org mode============================

;;enable org-mode
(require 'org)

;;make org-mode work with files ending in .org
(add-to-list 'auto-mode-alist '("\\.org$" . org-mode))

;;;========================org mode Capture============================
(setq org-directory "~/Ubuntu One/EmacsFilesUO/OrgFilesUO/")
(setq org-default-notes-file (concat org-directory "notes.org"))
    (define-key global-map "\C-cc" 'org-capture)

;;;org capture templates
(setq org-capture-templates
    ("n" "Notes" entry (file+datetree
               ,(concat org-directory "notes.org"))
   "* %^{Description} %^g %?
Added: %U")

;;;add more templates later
;;;create frame and close frame for capture
(defadvice org-capture-finalize
 (after delete-capture-frame activate)  
  "Advise capture-finalize to close the frame"  
  (if (equal "capture" (frame-parameter nil 'name))  
(defadvice org-capture-destroy
 (after delete-capture-frame activate)  
  "Advise capture-destroy to close the frame"  
  (if (equal "capture" (frame-parameter nil 'name))  
;; make the frame contain a single window. by default org-capture  
;; splits the window.  
(add-hook 'org-capture-mode-hook  
(defun make-capture-frame ()  
  "Create a new frame and run org-capture."  
  (make-frame '((name . "capture")
                (width . 120)
                (height . 15)))  
  (select-frame-by-name "capture")
  (setq word-wrap 1)
  (setq truncate-lines nil)

(require 'org-latex)
(unless (boundp 'org-export-latex-classes)
 (setq org-export-latex-classes nil))

;;;===============Org mode reftex ==================
;;;First, we want to load to load RefTeX whenever we use org-mode. 
;;;This is well documented, and mine only differs in the citation formats 
;;;..I pass to RefTex, and my additional key binding.
(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name) (file-exists-p (buffer-file-name))
	 ;enable auto-revert-mode to update reftex when bibtex file changes on disk
	 (global-auto-revert-mode t)
	 ;add a custom reftex cite format to insert links
	  '((?b . "[[bib:%l][%l-bib]]")
	    (?n . "[[notes:%l][%l-notes]]")
	    (?p . "[[papers:%l][%l-paper]]")
	    (?t . "%t")
	    (?h . "** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l-paper]]")))))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
  (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))

(add-hook 'org-mode-hook 'org-mode-reftex-setup)

;;;jump to entry
;;;The other difference I added was the binding of  ”C-c (” 
;;;to org-mode-reftex-search, which I defined earlier in my init.el. 
;;;This is the command that will jump to the entry in my org-mode file, and follows
(defun org-mode-reftex-search ()
  ;;jump to the notes for the paper pointed to at from reftex search
  (org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t))))


;; custom-set-variables was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(TeX-PDF-mode t t)
'(TeX-source-correlate-method (quote synctex))
'(TeX-source-correlate-mode t)
'(TeX-source-correlate-start-server t)
'(TeX-view-program-list (quote (("Okular" "okular --unique %o#src:%n%b"))))
'(TeX-view-program-selection (quote ((output-pdf "Okular") ((output-dvi style-pstricks) "dvips and gv") (output-dvi "xdvi") (output-html "xdg-open"))))

'(show-paren-mode t))
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(default ((t (:inherit nil :stipple nil :background "white" :foreground "black" :inverse-video nil :box nil :strike-through nil :overline nil :underline nil :slant normal :weight normal :height 98 :width normal :foundry "unknown" :family "Liberation Sans")))))

(setq TeX-auto-save t)
(setq TeX-parse-self t)
(setq TeX-save-query nil)


[-- Attachment #4: TestSciDocu.pdf --]
[-- Type: application/pdf, Size: 76589 bytes --]

[-- Attachment #5: TestSciDocu.org --]
[-- Type: application/octet-stream, Size: 928 bytes --]

#-*- mode: org -*-
The Impact of Beer Consumption on Scientific Collaboration
#+AUTHOR: Mario Fasold
#+LATEX_HEADER: \usepackage{natbib}

* Introduction
** Previous Work
Some studies relating scientific output and beer have previously been done.
In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance.

hi \citep{biswas2008generalized}
hello \citep{cai1992length}

* Results
** What beer should you drink
+ Becks
+ Czech Budweiser
+ Duff

Some example from a text file.

All lines between these markers are exported literally

Go to [[Introduction]]

x =\frac{a}{b}


       reply	other threads:[~2012-09-26 17:01 UTC|newest]

Thread overview: 10+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
     [not found] <CAL1SgUp87tichwJhr25VpnVTwniH+ivvoxoaiL_9oqFR-Ugcgg@mail.gmail.com>
2012-09-26 17:00 ` Sanjib Sikder [this message]
2012-09-26 18:38   ` Fwd: Citation in org mode does not compile Thomas S. Dye
2012-09-27  2:43     ` Sanjib Sikder
2012-09-27  3:14       ` Sanjib Sikder
2012-09-27  3:46         ` Yagnesh Raghava Yakkala
2012-09-27  3:59           ` Sanjib Sikder
2012-09-27  5:16             ` Yagnesh Raghava Yakkala
2012-09-27  5:28           ` Nick Dokos
2012-10-03  7:04       ` Nick Dokos
2012-10-03  9:40         ` Sanjib Sikder

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