From mboxrd@z Thu Jan 1 00:00:00 1970 From: Sharon Kimble Subject: Re: Bibliography woes! Date: Mon, 05 May 2014 18:08:52 +0100 Message-ID: <87r448xie3.fsf@skimble.plus.com> References: <8761lkfn2j.fsf@skimble.plus.com> <53678512.50602@gmail.com> <877g605lo4.fsf@skimble.plus.com> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36144) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WhMO5-0000Fu-W0 for emacs-orgmode@gnu.org; Mon, 05 May 2014 13:09:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1WhMO1-0001CG-BE for emacs-orgmode@gnu.org; Mon, 05 May 2014 13:09:09 -0400 Received: from avasout08.plus.net ([212.159.14.20]:34979) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WhMO0-0001CA-UG for emacs-orgmode@gnu.org; Mon, 05 May 2014 13:09:05 -0400 In-Reply-To: (Vikas Rawal's message of "Mon, 5 May 2014 17:07:36 +0200") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Vikas Rawal Cc: org-mode mailing list --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Vikas Rawal writes: >=20=20=20=20=20 > Any ideas please folks, or some code to try please? >=20=20=20=20=20 >=20=20=20=20=20 > > I use > > #+LATEX_HEADER: \usepackage > [citestyle=3Dauthoryear-icomp,bibstyle=3Dauthoryear,hyperref=3Dtrue,backr= ef=3Dtrue,maxcitenames=3D3,url=3Dtrue,backend=3Dbiber,natbib=3Dtrue]{biblat= ex} > > Can you try this, and if it works, modify as you prefer. > > Also, as Leonard suggested, I would create a tex file, and work on it > from the terminal to see what is wrong. > > Compile the tex file, run biber and then compile the tex file again. > This would help identify what is wrong. How do I do it from the command-line please? Using what commands? I can do it from inside org-mode, and I've created a test file and bib references, details now.=20 This is the test file =2D-8<---------------cut here---------------start------------->8--- # -*- mode:org; mode:reftex; indent-tabs-mode:nil; tab-width:2 -*- #+OPTIONS: toc:nil num:nil #+OPTIONS: ^:{} #+TITLE: Cat on the mat - 2014 #+AUTHOR: Sharon Kimble & Sarah ? #+LATEX_CLASS: article #+LATEX_CLASS_OPTIONS: [a4paper] #+LATEX_HEADER: \usepackage [citestyle=3Dauthoryear-icomp,bibstyle=3Dauthor= year,hyperref=3Dtrue,backref=3Dtrue,maxcitenames=3D3,url=3Dtrue,backend=3Db= iber,natbib=3Dtrue]{biblatex} # #+LATEX_HEADER: \usepackage[hyperref,x11names]{xcolor} # #+LATEX_HEADER: \usepackage[colorlinks=3Dtrue]{hyperref} #+LaTeX_HEADER: \usepackage{bussproofs} #+LaTeX_HEADER: \usepackage{amsmath,amssymb,amsopn} #+LaTeX_HEADER: \usepackage{graphicx} #+LaTeX_HEADER: \usepackage{makeidx} %robustindex % Indexing #+LaTeX_HEADER: \usepackage[british]{babel} % For british english hyphenati= on patterns #+LaTeX_HEADER: \usepackage{fancyhdr} % Change caption style; changes heade= rs and page styles # #+LaTeX_HEADER: \usepackage{biblatex} # #+LaTeX_HEADER: \usepackage[backend=3Dbibtex,style=3Dverbose]{biblatex} #+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/cat.bib} #+LaTeX_HEADER: \bibliography{references} \pagebreak * Chapter 1 Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy = nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi en= im ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl= ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrer= it in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit prae= sent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam lib= er tempor cum soluta nobis eleifend option congue nihil imperdiet doming id qu= od mazim placerat facer possim assum. Typi non habent claritatem insitam; est = usus legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam= processus dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare = quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum fo= rmas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. * Chapter 2 Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy = nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi en= im ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl= ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrer= it in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit prae= sent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam lib= er tempor cum soluta nobis eleifend option congue nihil imperdiet doming id qu= od mazim placerat facer possim assum. Typi non habent claritatem insitam; est = usus legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt lectores legere me lius quod ii legunt saepius. Claritas est etiam processus dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare = quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum fo= rmas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. * Bibliography \printbibliography * Index =2D-8<---------------cut here---------------end--------------->8--- and this is the bibliography file =2D-8<---------------cut here---------------start------------->8--- @Article{, author =3D {MacRae K. Pattison J.}, title =3D {Home chemotherapy.}, journaltitle =3D {Nursing Times}, year =3D {2002}, key =3D {1}, volume =3D {98}, number =3D {35}, pages =3D {34-35}, } =2D-8<---------------cut here---------------end--------------->8--- and this is the pdf output file =2D-8<---------------cut here---------------start------------->8--- This is XeTeX, Version 3.1415926-2.5-0.9999.3 (TeX Live 2013/Debian) \write18 enabled. entering extended mode (/home/boudiccas/.emacs.d/research/cat.tex LaTeX2e <2011/06/27> Babel <3.9k> and hyphenation patterns for 13 languages loaded. 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(.//cat.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/tipa/t3cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (.//cat.out) (.//cat.out) (.//cat.bbl) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1] LaTeX Warning: Citation '1' on page 2 undefined on input line 54. LaTeX Warning: Empty bibliography on input line 80. [2] (./cat.aux) LaTeX Warning: There were undefined references. Package biblatex Warning: Please (re)run Biber on the file: (biblatex) cat (biblatex) and rerun LaTeX afterwards. ) (see the transcript file for additional information) Output written on ./cat.pdf (2 pages). Transcript written on .//cat.log. =2D-8<---------------cut here---------------end--------------->8--- and this is from my "setup-testbed.el" =2D-8<---------------cut here---------------start------------->8--- ;;; XeTeX customisations ;; remove "inputenc" from default packages as it clashes with xelatex (setf org-latex-default-packages-alist (remove '("AUTO" "inputenc" t) org-latex-default-packages-alist)) ;; the sexp below will also work in this case. But it is not robust as it ;; pops the first element regardless if its a match or not. ;; (pop org-latex-default-packages-alist) (add-to-list 'org-latex-packages-alist '("" "xltxtra" t)) ;; choose Linux Libertine O as serif and Linux Biolinum O as sans-serif fon= ts (add-to-list 'org-latex-packages-alist '("" "libertine" t)) ;; commented for now as preferable to set per file for now ;; (add-to-list 'org-latex-packages-alist '("" "unicode-math" t)) ;; (add-to-list 'org-latex-packages-alist ;; "\\setmathfont{Linux Libertine}" t) ; needed for unicode-math ;; org to latex customisations, -shell-escape needed for minted (setq org-export-dispatch-use-expert-ui t ; non-intrusive export dispatch org-latex-pdf-process ; for regular export '("xelatex -shell-escape -interaction nonstopmode -output-directory %= o %f" "bibtex %b" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "bibtex %b" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "bibtex %b" "bibtex %b" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f")) ;; ;; export single chapter ;; (add-to-list 'org-latex-classes ;; '("chapter" "\\documentclass[11pt]{report}" ;; ("\\chapter{%s}" . "\\chapter*{%s}") ;; ("\\section{%s}" . "\\section*{%s}") ;; ("\\subsection{%s}" . "\\subsection*{%s}") ;; ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))) ;; ;; FIXME: doesn't work because of \hypersetup, \tableofcontents, etc. ;; ;; minimal export with the new exporter (maybe use the standalone class?) ;; (add-to-list 'org-latex-classes ;; '("minimal" ;; "\\documentclass\{minimal\}\n[NO-DEFAULT-PACKAGES]\n[NO-P= ACKAGES]" ;; ("\\section\{%s\}" . "\\section*\{%s\}") ;; ("\\subsection\{%s\}" . "\\subsection*\{%s\}") ;; ("\\subsubsection\{%s\}" . "\\subsubsection*\{%s\}"))) (defun my-auto-tex-parameters () "Automatically select the tex packages to include." ;; default packages for ordinary latex or pdflatex export (setq org-export-latex-default-packages-alist '(("AUTO" "inputenc" t) ("T1" "fontenc" t) ("" "fixltx2e" nil) ("" "wrapfig" nil) ("" "soul" t) ("" "textcomp" t) ("" "marvosym" t) ("" "wasysym" t) ("" "latexsym" t) ("" "amssymb" t) ("" "hyperref" nil))) ;; Packages to include when xelatex is used (if (string-match "LATEX_CMD: xelatex" (buffer-string)) (setq org-export-latex-default-packages-alist '(("" "fontspec" t) ("" "xunicode" t) ("" "url" t) ("" "rotating" t) ("british" "babel" t) ("babel" "csquotes" t) ("" "soul" t) ("xetex" "hyperref" nil) ))) (if (string-match "LATEX_CMD: xelatex" (buffer-string)) (setq org-export-latex-classes (cons '("article" "\\documentclass[11pt,article,oneside]{memoir}" ("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" . "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}") ("\\paragraph{%s}" . "\\paragraph*{%s}") ("\\subparagraph{%s}" . "\\subparagraph*{%s}")) org-export-latex-classes)))) (add-hook 'org-export-latex-after-initial-vars-hook 'my-auto-tex-parameters) =2D-8<---------------cut here---------------end--------------->8--- To create a tex file I have used "C-c C-e l l" To create the pdf file I did "C-c C-e l p" I've given all the information that I can such that you can use the same files and recreate my pdf. The problems that I am finding is the bibliography is not displayed in the pdf file, but I don't know why. Hopefully with all of this information we can work out where I'm going wrong? Thanks Sharon. =2D-=20 A taste of linux =3D http://www.sharons.org.uk my git repo =3D https://bitbucket.org/boudiccas/dots TGmeds =3D http://www.tgmeds.org.uk Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19 --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJTZ8WlAAoJEDaBgBkK+INbgXoP/0LvsM0BCp3D+44EbKv6e91i bKIVyKOHBL2PKWr4t9o62mJzgMEufbe1/AC94nDF7N3D1Vf6UrHcF6IfVNeoNLWW +sBVlsBl0C7Wr/x4UTOGvGs5JDJVgQlbYkyxWJ8ePxm4MyiLGQAj03enU0GsmTUX dOGgGGRodSSkBouVS5IkFEWLHkWlBnypR5MjE18wy8wUne2ZZzXXaKYPqn0iyj9Y aGD/Y1xdjYUjCZyBWNa5/M2Oo4NDJ9ej6hntDB3i72FEOZlthYsoFfvdjMEo/yZD PltDK9y8+CPlHVkcPuY8s/r2hQFtpBHRRH63TlgALq7Nx2jHhAISbGDZEFPm/u3X DTks7qlkK/JAp+qKKN7j9ythLBel2j0RbgG1fP90hJCAXAafm3WFSyylKe+cJqXL UDILtO9L0aPSBmDjR2xl1k4MejEloXLGmp/prHaOr67eVvYUCuIt/WqghzAsjtDB lq2C+RXMERmhHLpwjkdNJmFd6Hck9HPbZ14/usK9LlTD5FZG7P+pYTJBSkCZNZi6 OWrh95gew7x/O3+YmHenOm7PZ19j4UkhhgoxZdIIIDrUvNTHy/oI1KjrwNIDlX3r XDfBBQDxgiK9TkFeSc4H+IfUQsr2tXIhKW2bXv8LVpz30asYNTqfhd+r8/2Pl0Ir NIU6erSTRa1vhOjpbOfT =qdqD -----END PGP SIGNATURE----- --=-=-=--