Hi,

I was trying to manage my technical journal papers using Orgmode.
I followed instructions from the following links

http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/
http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/

I have three files
1. bibliography file with extension .bib (bibPhD.bib)
2. one list file where I save names of papers etc with .org extension
(bibListDrBx.org)
3. one notes file with .org extension where I write notes related to papers
listed in item 2 (bibNotesDrBx.org)

There are links with rtcite , so that i can jump from one file to another
at desired location.

The following is the content of bibNotesDrBx.org
---------------------------------------------------------------
#+LINK: biblist
rtcite:~/Dropbox/OrgDrBx/ResearchDrBx/BibListOrgDrBx/bibListDrBx.org::#%s
#+LINK: bib rtcite:~/Dropbox/OrgDrBx/ResearchDrBx/BibDrBx/bibPhD.bib::%s
# \bibliography{~/Dropbox/OrgDrBx/ResearchDrBx/BibDrBx/bibPhD}


** Name of one of the paper :mytag:
:PROPERTIES:
:Custom_ID: paper2012
:END:    [[papers:paper2012][paper2012-paper]]
[[bib:paper2012][paper2012-bib]]    [[biblist:paper2012][paper2012-biblist]]


--------------------------------------------------------------
The above file works fine. It can connect with other files perfectly. It
can make pdf wth C-c C-e p.
--------------------------------------------------------------
Problem is in the following file bibListDrBx.org
The following is the content of bibListDrBx.org file
-----------------------------------------------------------------

Research Notes
#+STARTUP: indent hidestars
#+TITLE: Research Notes
#+LINK: notes
rtcite:~/Dropbox/OrgDrBx/ResearchDrBx/BibNotesOrgDrBx/bibNotesDrBx.org::#%s
#+LINK: bib rtcite:~/Dropbox/OrgDrBx/ResearchDrBx/BibDrBx/bibPhD.bib::%s
#+TODO: TODO | DONE
#+TODO: HOLD | HALT
#+title: My Title
#+author: My Name
# \bibliography{~/Dropbox/OrgDrBx/ResearchDrBx/BibDrBx/bibPhD}
* Tasks
* Research :Research:
* Papers :paper:
** Name of my journal entry
:PROPERTIES:
:Custom_ID: paper2012
:END:
[[papers:paper2012][paper2012-paper]]    [[bib:paper2012][paper2012-bib]]
** Other Papers
* Resources
* Data
\bibliography{~/Dropbox/OrgDrBx/ResearchDrBx/BibDrBx/bibPhD}{}
\bibliographystyle{plain}
-------------------------------------------------------------------------------------------------------------
This file also successfully connects with pdf and other files.
Problem is, when I press C c C e p to make pdf of the file bibListDrBx.org
, it says *"Symbol's function definition is void: search"*

i have located the lines which are causing error.
and those are
** Name of my journal entry
:PROPERTIES:
:Custom_ID: paper2012
:END:
[[papers:paper2012][paper2012-paper]]    [[bib:paper2012][paper2012-bib]]

Now these lines were there in my bibNotesDrBx.org files also and I have no
issue in making pdf of that file. What is wrong with the other file
(bibListDrBx.org)  ?


---------------------------------
Following is my .emacs set up
-----------------------------------
;;Last updated : 28 Sep2012: 12:26 AM



(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 ()
    'turn-on-font-lock
    (setq word-wrap 1)
    (setq truncate-lines nil)
    (flyspell-mode 1)))

;;;=================================================
;;predictive
(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============================
;;;..............................................................
;;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))
    (delete-frame)))

(defadvice org-capture-destroy
(after delete-capture-frame activate)
"Advise capture-destroy to close the frame"
(if (equal "capture" (frame-parameter nil 'name))
    (delete-frame)))

;; make the frame contain a single window. by default org-capture
;; splits the window.
(add-hook 'org-capture-mode-hook
        'delete-other-windows)

(defun make-capture-frame ()
"Create a new frame and run org-capture."
(interactive)
(make-frame '((name . "capture")
              (width . 120)
              (height . 15)))
(select-frame-by-name "capture")
(setq word-wrap 1)
(setq truncate-lines nil)
(org-capture))


;;;============================
(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))
     (progn
    ;enable auto-revert-mode to update reftex when bibtex file changes on
disk
    (global-auto-revert-mode t)
    (reftex-parse-all)
    ;add a custom reftex cite format to insert links
    (reftex-set-cite-format
    '((?b . "[[bib:%l][%l-bib]]")
      (?p . "[[papers:%l][%l-paper]]")
      (?n . "** %t\n:PROPERTIES:\n:Custom_ID:
%l\n:END:\t[[papers:%l][%l-paper]]\t[[bib:%l][%l-bib]]\t[[biblist:%l][%l-biblist]]")
      (?t . "%t")
      (?h . "** %t\n:PROPERTIES:\n:Custom_ID:
%l\n:END:\n[[papers:%l][%l-paper]]\t[[bib:%l][%l-bib]]\t[[notes:%l][%l-note]]")))))
(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
(interactive)
(org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t))))
;;;............................
;;;;;link files in reference notes
(setq org-link-abbrev-alist
     '(("bib" . "~/Research/Bib/bibliography.bib::%s")
   ("notes" . "~/Research/Notes/Org/notes.org::#%s")
   ("papers" . "~/Research/Papers/%s.pdf")))
;;;........................................................
;;;; notes for references and linking with rtcite
(defun my-rtcite-export-handler (path desc format)
 (message "my-rtcite-export-handler is called : path = %s, desc = %s,
format = %s" path desc format)
 (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
                  (match-string 1 path)))
        (path (substring path 0 (match-beginning 0))))
    (cond ((eq format 'latex)
          (if (or (not desc)
                  (equal 0 (search "rtcite:" desc)))
              (format "\\cite{%s}" search)
            (format "\\cite[%s]{%s}" desc search))))))


(require 'org)

(org-add-link-type "rtcite"
                  'org-bibtex-open
                  'my-rtcite-export-handler)

;;;=============================================
;;;org mode latex to pdf export
(setq org-latex-to-pdf-process
     '("pdflatex -interaction nonstopmode %b"
       "/usr/bin/bibtex %b"
       "pdflatex -interaction nonstopmode %b"
       "pdflatex -interaction nonstopmode %b"))

;;;===========Latex==============

(custom-set-variables
;; 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
;; 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)





;;;==================================================




Thanks :)

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

*