* Bibliography woes!
@ 2014-05-05 12:05 Sharon Kimble
2014-05-05 12:26 ` Vikas Rawal
2014-05-05 12:33 ` Leonard Avery Randall
0 siblings, 2 replies; 16+ messages in thread
From: Sharon Kimble @ 2014-05-05 12:05 UTC (permalink / raw)
To: org-mode
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I'm having no success in getting the bibliography to display in my
document, so these are my relevant settings -
╭────
│#+LaTeX_HEADER: \usepackage{biblatex}
│#+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/references.bib}
│#+LaTeX_HEADER: \bibliography{references}
╰────
and I'm using XeTeX, Version 3.1415926-2.5-0.9999.3 (TeX Live 2013/Debian)
Where I want to have the bibliography is -
╭────
│* Bibliography
│\printbibliography
╰────
and I generate my .tex and .pdf files by "C-c C-e l p" but the
bibliography is not displayed in the pdf.
In the *messages* pane, is shown "Process completed with errors:
[undefined citation] [LaTeX error]"
And in "org-pdf-latex-output" it shows this -
--8<---------------cut here---------------start------------->8---
LaTeX Warning: Citation '4' on page 3 undefined on input line 139.
LaTeX Warning: Citation '5' on page 3 undefined on input line 141.
LaTeX Warning: Citation '4' on page 3 undefined on input line 149.
LaTeX Warning: Citation '6' on page 3 undefined on input line 158.
[3]
LaTeX Warning: Citation '7' on page 4 undefined on input line 171.
--8<---------------cut here---------------end--------------->8---
But "page 3" of what? "input line 139" of what? Citation 3 is here
--8<---------------cut here---------------start------------->8---
@Article{,
author = {MacRae K. Pattison J.},
title = {Home chemotherapy.},
journaltitle = {Nursing Times},
year = {2002},
key = {3},
volume = {98},
number = {35},
pages = {34-35},
}
--8<---------------cut here---------------end--------------->8---
It all looks okay to me, except I cant see what the latex warnings
relate to. Any ideas folks please?
Thanks
Sharon.
--
A taste of linux = http://www.sharons.org.uk
my git repo = https://bitbucket.org/boudiccas/dots
TGmeds = http://www.tgmeds.org.uk
Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19
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^ permalink raw reply [flat|nested] 16+ messages in thread* Re: Bibliography woes! 2014-05-05 12:05 Bibliography woes! Sharon Kimble @ 2014-05-05 12:26 ` Vikas Rawal 2014-05-05 12:33 ` Leonard Avery Randall 1 sibling, 0 replies; 16+ messages in thread From: Vikas Rawal @ 2014-05-05 12:26 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode mailing list > I'm having no success in getting the bibliography to display in my > document, so these are my relevant settings - > ╭──── > │#+LaTeX_HEADER: \usepackage{biblatex} > │#+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/references.bib} > │#+LaTeX_HEADER: \bibliography{references} > ╰──── Although I cannot be sure, it seems to me that the problem may be that biblatex is not looking for references.bib in the right place. I had similar trouble when I started using citations (then with bibtex). I then solved it by create a link to the bib file in the working directory, and continue to use that solution for everything I write. In your working directory, where you org file is, just create a symbolic link: ln -s /home/boudiccas/.emacs.d/research/references.bib references.bib If my diagnosis is correct, that should solve the problem. Vikas ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 12:05 Bibliography woes! Sharon Kimble 2014-05-05 12:26 ` Vikas Rawal @ 2014-05-05 12:33 ` Leonard Avery Randall 2014-05-05 14:45 ` Sharon Kimble 1 sibling, 1 reply; 16+ messages in thread From: Leonard Avery Randall @ 2014-05-05 12:33 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode [-- Attachment #1: Type: text/plain, Size: 957 bytes --] Hi, Sharon Kimble wrote: > > But "page 3" of what? "input line 139" of what? Page 3 of the PDF and input line 139 of the .tex file. > > It all looks okay to me, except I cant see what the latex warnings > relate to. Any ideas folks please? The most likely problem is that you have you have not called bibtex (or biber) the appropriate number of times and so your references have not been processed correctly. The way to check this is to run bibtex or biber (whichever you use, your setup looks like it was designed for bibtex so bibtex is probably the one you want) on your .tex file and then call xelatex again, and see if the errors go away. If that is the problem. You should look at how you have set up org-latex-pdf-process to make sure that it calls xelatex and bibtex the appropriate number of times. (another option is to use latexmk, it is really convenient, but it takes a bit of work to configure it properly). All best, Leonard [-- Attachment #2: Type: text/html, Size: 1402 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 12:33 ` Leonard Avery Randall @ 2014-05-05 14:45 ` Sharon Kimble 2014-05-05 15:07 ` Vikas Rawal 0 siblings, 1 reply; 16+ messages in thread From: Sharon Kimble @ 2014-05-05 14:45 UTC (permalink / raw) To: Leonard Avery Randall; +Cc: org-mode [-- Attachment #1: Type: text/plain, Size: 4477 bytes --] Leonard Avery Randall <leonard.a.randall@gmail.com> writes: > Hi, > > Sharon Kimble wrote: > > But "page 3" of what? "input line 139" of what? > > > Page 3 of the PDF and input line 139 of the .tex file. > > It all looks okay to me, except I cant see what the latex warnings > relate to. Any ideas folks please? > > > The most likely problem is that you have you have not called bibtex > (or biber) the appropriate number of times and so your references have > not been processed correctly. The way to check this is to run bibtex > or biber (whichever you use, your setup looks like it was designed for > bibtex so bibtex is probably the one you want) on your .tex file and > then call xelatex again, and see if the errors go away. If that is the > problem. You should look at how you have set up org-latex-pdf-process > to make sure that it calls xelatex and bibtex the appropriate number > of times. (another option is to use latexmk, it is really convenient, > but it takes a bit of work to configure it properly). > Still not getting it right. This is in my "setup-testbed.el" --8<---------------cut here---------------start------------->8--- ;; 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" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f")) --8<---------------cut here---------------end--------------->8--- and the partial transcript of the output log --8<---------------cut here---------------start------------->8--- LaTeX Warning: Citation '4' on page 3 undefined on input line 135. LaTeX Warning: Citation '5' on page 3 undefined on input line 137. LaTeX Warning: Citation '4' on page 3 undefined on input line 145. LaTeX Warning: Citation '6' on page 3 undefined on input line 154. LaTeX Warning: Citation '7' on page 4 undefined on input line 167. LaTeX Warning: Citation '8' on page 4 undefined on input line 175. LaTeX Warning: Citation '12' on page 4 undefined on input line 204. LaTeX Warning: Citation '7' on page 4 undefined on input line 209. LaTeX Warning: Citation '9' on page 4 undefined on input line 222. LaTeX Warning: Citation '1' on page 5 undefined on input line 259. LaTeX Warning: Citation '3' on page 6 undefined on input line 285. LaTeX Warning: Citation '10' on page 7 undefined on input line 349. LaTeX Warning: Citation '10' on page 7 undefined on input line 400. LaTeX Warning: Citation '13' on page 9 undefined on input line 458. LaTeX Warning: Citation '11' on page 9 undefined on input line 475. LaTeX Warning: Citation '14' on page 9 undefined on input line 495. LaTeX Warning: Citation '14' on page 10 undefined on input line 527. LaTeX Warning: Citation '2' on page 11 undefined on input line 569. LaTeX Warning: Empty bibliography on input line 576. [11] (./uh2014.aux) LaTeX Warning: There were undefined references. Package biblatex Warning: Please (re)run Biber on the file: (biblatex) uh2014 (biblatex) and rerun LaTeX afterwards. --8<---------------cut here---------------end--------------->8--- and in my org-mode file I have these headers --8<---------------cut here---------------start------------->8--- #+LaTeX_HEADER: \usepackage{biblatex} #+LaTeX_HEADER: \usepackage[backend=biber,style=verbose]{biblatex} #+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/references.bib} #+LaTeX_HEADER: \bibliography{references} --8<---------------cut here---------------end--------------->8--- I have created the link to the reference file in my $USER/.emacs.d/org/ directory using this command ╭──── │ln -s /home/boudiccas/.emacs.d/research/references.bib references.bib ╰──── Any ideas please folks, or some code to try please? Thanks Sharon. -- A taste of linux = http://www.sharons.org.uk my git repo = https://bitbucket.org/boudiccas/dots TGmeds = http://www.tgmeds.org.uk Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 818 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 14:45 ` Sharon Kimble @ 2014-05-05 15:07 ` Vikas Rawal 2014-05-05 15:48 ` Leonard Avery Randall 2014-05-05 17:08 ` Sharon Kimble 0 siblings, 2 replies; 16+ messages in thread From: Vikas Rawal @ 2014-05-05 15:07 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode mailing list [-- Attachment #1: Type: text/plain, Size: 532 bytes --] > > Any ideas please folks, or some code to try please? > I use #+LATEX_HEADER: \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} 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. Vikas [-- Attachment #2: Type: text/html, Size: 1235 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 15:07 ` Vikas Rawal @ 2014-05-05 15:48 ` Leonard Avery Randall 2014-05-05 17:08 ` Sharon Kimble 1 sibling, 0 replies; 16+ messages in thread From: Leonard Avery Randall @ 2014-05-05 15:48 UTC (permalink / raw) To: Vikas Rawal; +Cc: org-mode mailing list, Sharon Kimble [-- Attachment #1: Type: text/plain, Size: 218 bytes --] Hi Sharon, Your setup seems to only call bibtex once. I find that with biblatex this is usually not enough to resolve references. I would call bibtex a second time after the second run of biblatex. All best, Leonard [-- Attachment #2: Type: text/html, Size: 395 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 15:07 ` Vikas Rawal 2014-05-05 15:48 ` Leonard Avery Randall @ 2014-05-05 17:08 ` Sharon Kimble 2014-05-05 18:26 ` Eric S Fraga 1 sibling, 1 reply; 16+ messages in thread From: Sharon Kimble @ 2014-05-05 17:08 UTC (permalink / raw) To: Vikas Rawal; +Cc: org-mode mailing list [-- Attachment #1: Type: text/plain, Size: 20149 bytes --] Vikas Rawal <vikaslists@agrarianresearch.org> writes: > > Any ideas please folks, or some code to try please? > > > > I use > > #+LATEX_HEADER: \usepackage > [citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} > > 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. This is the test file --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=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} # #+LATEX_HEADER: \usepackage[hyperref,x11names]{xcolor} # #+LATEX_HEADER: \usepackage[colorlinks=true]{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 hyphenation patterns #+LaTeX_HEADER: \usepackage{fancyhdr} % Change caption style; changes headers and page styles # #+LaTeX_HEADER: \usepackage{biblatex} # #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{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 enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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 formas 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 enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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 formas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. * Bibliography \printbibliography * Index --8<---------------cut here---------------end--------------->8--- and this is the bibliography file --8<---------------cut here---------------start------------->8--- @Article{, author = {MacRae K. Pattison J.}, title = {Home chemotherapy.}, journaltitle = {Nursing Times}, year = {2002}, key = {1}, volume = {98}, number = {35}, pages = {34-35}, } --8<---------------cut here---------------end--------------->8--- and this is the pdf output file --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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Version 1.1. ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/xebabel.def))) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) Package Babel Warning: The package option `english' should not be used (Babel) with a more specific one (like `british') on input line 27. (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/se-ascii-print.def) (/usr/share/texlive/texmf-dist/tex/latex/biblatex/lbx/english.lbx) Package biblatex Warning: 'babel/polyglossia' detected but 'csquotes' missing. (biblatex) Loading 'csquotes' recommended. (.//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. --8<---------------cut here---------------end--------------->8--- and this is from my "setup-testbed.el" --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 fonts (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-PACKAGES]" ;; ("\\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) --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. -- A taste of linux = http://www.sharons.org.uk my git repo = https://bitbucket.org/boudiccas/dots TGmeds = http://www.tgmeds.org.uk Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 818 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 17:08 ` Sharon Kimble @ 2014-05-05 18:26 ` Eric S Fraga 2014-05-05 22:23 ` Sharon Kimble 0 siblings, 1 reply; 16+ messages in thread From: Eric S Fraga @ 2014-05-05 18:26 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode mailing list, Vikas Rawal On Monday, 5 May 2014 at 18:08, Sharon Kimble wrote: [...] > 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. Sharon, have you not seen my other email? Your problem is the actual bibtex entry is wrong, missing the label that is needed to be able to cite it in LaTeX. [...] > lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam processus [...] > and this is the bibliography file > @Article{, change this line to @Article{1, although I would recommend a more description label personally... -- : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11 ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 18:26 ` Eric S Fraga @ 2014-05-05 22:23 ` Sharon Kimble 2014-05-05 23:39 ` John Hendy 2014-05-05 23:47 ` Bibliography woes! Leonard Avery Randall 0 siblings, 2 replies; 16+ messages in thread From: Sharon Kimble @ 2014-05-05 22:23 UTC (permalink / raw) To: Vikas Rawal, Eric S Fraga; +Cc: org-mode mailing list [-- Attachment #1.1: Type: text/plain, Size: 1133 bytes --] Eric S Fraga <e.fraga@ucl.ac.uk> writes: > On Monday, 5 May 2014 at 18:08, Sharon Kimble wrote: > > [...] > >> 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. > > Sharon, have you not seen my other email? Your problem is the actual > bibtex entry is wrong, missing the label that is needed to be able to > cite it in LaTeX. > I'd sent my reply before getting and reading your email, sorry Eric. > > [...] > >> lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam processus > > [...] > >> and this is the bibliography file >> @Article{, > > change this line to > > @Article{1, > > although I would recommend a more description label personally... I've set it up with the articles author and year, but it is still failing. I'm attaching the original org file, the generated tex and pdf, and the bib file. Hopefully this will help find a solution? Thanks Sharon. --8<---------------cut here---------------start------------->8--- Attachments [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1.2: cat.tex --] [-- Type: text/x-tex, Size: 3791 bytes --] % Created 2014-05-05 Mon 23:14 \documentclass[a4paper]{article} \usepackage[T1]{fontenc} \usepackage{fixltx2e} \usepackage{graphicx} \usepackage{longtable} \usepackage{float} \usepackage{wrapfig} \usepackage{rotating} \usepackage[normalem]{ulem} \usepackage{amsmath} \usepackage{textcomp} \usepackage{marvosym} \usepackage[nointegrals]{wasysym} \usepackage{amssymb} \usepackage{hyperref} \tolerance=1000 \usepackage{libertine} \usepackage{xltxtra} \usepackage{amsmath} \usepackage{bussproofs} \usepackage{amsmath,amssymb,amsopn} \usepackage{graphicx} \usepackage{makeidx} %robustindex % Indexing \usepackage[british, english]{babel} % For british english hyphenation patterns \usepackage{fancyhdr} % Change caption style; changes headers and page styles \usepackage{biblatex} \bibliography{/home/boudiccas/.emacs.d/research/cat.bib} \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} \bibliography{references} \author{Sharon Kimble \& Sarah ?} \date{\today} \title{Cat on the mat - 2014} \hypersetup{ pdfkeywords={}, pdfsubject={}, pdfcreator={Emacs 24.4.50.19 (Org mode 8.2.6)}} \begin{document} \maketitle \pagebreak \section*{Chapter 1} \label{sec-1} Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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{MacRae K, et al;2002}. Claritas est etiam processus dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. \section*{Chapter 2} \label{sec-2} Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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 formas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. \section*{Bibliography} \label{sec-3} \printbibliography \section*{Index} \label{sec-4} % Emacs 24.4.50.19 (Org mode 8.2.6) \end{document} [-- Attachment #1.3: cat.pdf --] [-- Type: application/pdf, Size: 18086 bytes --] [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1.4: cat.bib --] [-- Type: text/x-bibtex, Size: 235 bytes --] @Article{MacRae K, et al;2002, author = {MacRae K. Pattison J.}, title = {Home chemotherapy.}, journaltitle = {Nursing Times}, year = {2002}, key = {1}, volume = {98}, number = {35}, pages = {34-35}, } [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1.5: cat.org --] [-- Type: text/x-org, Size: 3608 bytes --] # -*- 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{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 hyphenation patterns #+LaTeX_HEADER: \usepackage{fancyhdr} % Change caption style; changes headers and page styles #+LaTeX_HEADER: \usepackage{biblatex} #+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/cat.bib} #+LATEX_HEADER: \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} #+LaTeX_HEADER: \bibliography{references} # #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{biblatex} # #+LATEX_HEADER: \usepackage[hyperref,x11names]{xcolor} # #+LATEX_HEADER: \usepackage[colorlinks=true]{hyperref} \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 enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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{MacRae K, et al;2002}. Claritas est etiam processus dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas 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 enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod 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 formas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum. * Bibliography \printbibliography * Index [-- Attachment #1.6: Type: text/plain, Size: 260 bytes --] --8<---------------cut here---------------end--------------->8--- -- A taste of linux = http://www.sharons.org.uk my git repo = https://bitbucket.org/boudiccas/dots TGmeds = http://www.tgmeds.org.uk Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 818 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 22:23 ` Sharon Kimble @ 2014-05-05 23:39 ` John Hendy 2014-05-05 23:51 ` Ken Mankoff 2014-05-06 14:13 ` Bibliography woes! SOLVED Sharon Kimble 2014-05-05 23:47 ` Bibliography woes! Leonard Avery Randall 1 sibling, 2 replies; 16+ messages in thread From: John Hendy @ 2014-05-05 23:39 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode mailing list, Vikas Rawal [-- Attachment #1: Type: text/plain, Size: 4140 bytes --] On Mon, May 5, 2014 at 5:23 PM, Sharon Kimble <boudiccas@skimble.plus.com> wrote: > Eric S Fraga <e.fraga@ucl.ac.uk> writes: > [...] >> >>> and this is the bibliography file >>> @Article{, >> >> change this line to >> >> @Article{1, >> >> although I would recommend a more description label personally... > > I've set it up with the articles author and year, but it is still > failing. I'm attaching the original org file, the generated tex and > pdf, and the bib file. Hopefully this will help find a solution? I've been following this from a distance, as I'm interested in eventually getting into this. I would kindly ask that you slow down your pace, check things over, and proceed *simply* to solve your problem. Eric advocated using @Article{1, ... Without ever having used biblatex, I immediately wondered whether a comma delimited bibliography would tolerate: @Article{MacRae K, et al;2002, ... The answer is that it will not. You also have multiple lines loading the same package: #+LaTeX_HEADER: \usepackage{biblatex} #+LATEX_HEADER: \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} # #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{biblatex} Lastly, I would highly suggest limiting your requests for help to extremely simple examples. For example, remove packages that do not affect the behavior of the problem, such as bussproofs, babel, fancyhdr, etc. I was able to get your file working via the following method: - Modified cat.bib: @Article{1, author = {MacRae K. Pattison J.}, title = {Home chemotherapy.}, journaltitle = {Nursing Times}, year = {2002}, key = {1}, volume = {98}, number = {35}, pages = {34-35}, } - Modified/shortened/simplified cat.org: # -*- mode:org; mode:reftex; indent-tabs-mode:nil; tab-width:2 -*- #+OPTIONS: toc:nil num:nil ^:{} #+TITLE: Cat on the mat - 2014 #+AUTHOR: Sharon Kimble & Sarah ? #+LATEX_CLASS: article #+LATEX_CLASS_OPTIONS: [a4paper] #+LaTeX_HEADER: \usepackage[backend=biber,style=verbose,style=numeric]{biblatex} #+LaTeX_HEADER: \bibliography{/home/jwhendy/Downloads/cat.bib} %%% <- change this path #+LaTeX_HEADER: \bibliography{cat * Chapter 1 Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat.\cite{1} * Bibliography \printbibliography Note that you needed to load biblatex before your bibliography (which you sort of did, but then re-loaded it with a bunch of options and then perhaps again at the end depending on how Org deals with the # symbol before #+ lines. You can tweak the options to biblatex however you'd like; I just simplified a bit to single down to one line loading it. \bibliography needed to call the file cat, not bibliography. In addition, I had to run C-c C-e l p to export to latex, then check the buffer *Org PDF LaTeX Output* for messages regarding the failed citation. It suggested to run biber on the file cat, which I did from the command line. # note that I saved all your stuff in my download folder $ cd ~/Downloads $ biber cat Make sure you have the biber executable installed. I didn't know anything about it and thought biblatex might provide it. I had to explicitly install biber. You should be a path as the response to the following if you have it: $ which biber Running biber generated .bbl. Then, re-running C-c C-e l p from Org works for me (at least I think; see attached to verify). Lastly, when I encountered an error, I googled to find out what to do: - Using biber: http://tex.stackexchange.com/questions/26516/how-to-use-biber - Why \bibliography was giving me an error: http://kb.mit.edu/confluence/pages/viewpage.action?pageId=3907111 If this works, someone can chime in regarding how to modify Org so that it will run the necessary biber/biblatex commands so you don't have to jump to a command line every time. Or perhaps that's a one time thing -- maybe as long as biber generates the .bbl file, you can refer to anything you want in that file from then on? Hope that helps, John [-- Attachment #2: cat-jwhendy.pdf --] [-- Type: application/pdf, Size: 74325 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 23:39 ` John Hendy @ 2014-05-05 23:51 ` Ken Mankoff 2014-05-06 7:33 ` Rainer M Krug 2014-05-06 14:13 ` Bibliography woes! SOLVED Sharon Kimble 1 sibling, 1 reply; 16+ messages in thread From: Ken Mankoff @ 2014-05-05 23:51 UTC (permalink / raw) To: John Hendy; +Cc: org-mode mailing list, Vikas Rawal, Sharon Kimble On 2014-05-05 at 19:39, John Hendy wrote: > If this works, someone can chime in regarding how to modify Org so > that it will run the necessary biber/biblatex commands so you don't > have to jump to a command line every time. Or perhaps that's a one > time thing -- maybe as long as biber generates the .bbl file, you can > refer to anything you want in that file from then on? I've found "latexmk" to be the best tool for compiling LaTeX documents. It runs all necessary commands as many times as needed, including pdflatex, bibtex, biblatex, etc.. It is fairly smart and will run the command to make the index if you load the index, for example. It can run in daemon mode and monitor the included files (and graphics) so if one of those changes, the PDF is regenerated. I prefer daemon mode, so I bring up a terminal and run latexmk file.tex in the folder where I'm working on file.org. This also speeds things up, since exporting to latex is fast, but compiling is slow. I can export and still use emacs, rather than waiting for the compile to finish. But if you want to run latexmk from Org, that works too. The "-pvc-" turns off the "preview continuous" mode (daemon). (setq org-latex-pdf-process (list "/usr/texbin/latexmk -f -gg -pvc- %f")) -k. ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 23:51 ` Ken Mankoff @ 2014-05-06 7:33 ` Rainer M Krug 2014-05-06 11:25 ` Ken Mankoff 0 siblings, 1 reply; 16+ messages in thread From: Rainer M Krug @ 2014-05-06 7:33 UTC (permalink / raw) To: Ken Mankoff; +Cc: org-mode mailing list, Vikas Rawal, Sharon Kimble [-- Attachment #1: Type: text/plain, Size: 1933 bytes --] Ken Mankoff <mankoff@gmail.com> writes: > On 2014-05-05 at 19:39, John Hendy wrote: >> If this works, someone can chime in regarding how to modify Org so >> that it will run the necessary biber/biblatex commands so you don't >> have to jump to a command line every time. Or perhaps that's a one >> time thing -- maybe as long as biber generates the .bbl file, you can >> refer to anything you want in that file from then on? > > I've found "latexmk" to be the best tool for compiling LaTeX > documents. It runs all necessary commands as many times as needed, > including pdflatex, bibtex, biblatex, etc.. It is fairly smart and will > run the command to make the index if you load the index, for example. > > It can run in daemon mode and monitor the included files (and graphics) > so if one of those changes, the PDF is regenerated. > > I prefer daemon mode, so I bring up a terminal and run latexmk file.tex > in the folder where I'm working on file.org. This also speeds things up, > since exporting to latex is fast, but compiling is slow. I can export > and still use emacs, rather than waiting for the compile to finish. This sounds very interesting. Could you please provide some details on how you use latexmk? Do you use any special options? Rainer > > But if you want to run latexmk from Org, that works too. The "-pvc-" > turns off the "preview continuous" mode (daemon). > > (setq org-latex-pdf-process (list "/usr/texbin/latexmk -f -gg -pvc- %f")) > > -k. > -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer@krugs.de Skype: RMkrug PGP: 0x0F52F982 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-06 7:33 ` Rainer M Krug @ 2014-05-06 11:25 ` Ken Mankoff 2014-05-06 11:40 ` Rainer M Krug 0 siblings, 1 reply; 16+ messages in thread From: Ken Mankoff @ 2014-05-06 11:25 UTC (permalink / raw) To: Rainer M Krug; +Cc: org-mode mailing list, Vikas Rawal, Sharon Kimble On 2014-05-06 at 03:33, Rainer M Krug wrote: > Ken Mankoff <mankoff@gmail.com> writes: >> I've found "latexmk" to be the best tool for compiling LaTeX >> documents. > > This sounds very interesting. Could you please provide some details on > how you use latexmk? Do you use any special options? My ~/.latexmkrc file is below. It appears I have extra functions for making glossaries and working with PythonTeX. There is plenty of support for latexmk on TeX.SE https://tex.stackexchange.com/questions/tagged/latexmk Since I turn on preview_continuous_mode in my ~/.latexmkrc, I need to explicitly turn it off if I am calling latexmk from Org, hence the "-pvc-" option here: (setq org-latex-pdf-process (list "/usr/texbin/latexmk -f -gg -pvc- %f")) But as I said, I find I prefer to bring up a terminal in the directory where I am working, and dedicate it to running 'latexmk' in continuous monitoring mode. When I want to clean up a project I'll run "latexmk -c file.tex" to discard all of the temporary files. I have Skim.app or Preview.app (OS X PDF viewers) open the PDF file. I edit Org files, export to LaTeX (C-c C-e l l), and then keep working while the PDF regenerates. -k. # BEGIN ~/.latexmkrc $pdf_mode = 1; $preview_continuous_mode = 1; $new_viewer_always = 1; $silent = 1; # don't stop on errors $verbose = 0; #$halt_on_error = 1; $clean_ext = 'bbl run.xml %R-blx.bib acn glo xdy synctex.gz'; # continue past errors $force_mode = 1; $shell_escape = 1; # shell escape $pdflatex = 'pdflatex --shell-escape -file-line-error -synctex=1 %O %S'; # $pdf_previewer = 'open -a /Applications/Preview.app'; $pdf_previewer = 'open -a /Users/mankoff/local/Applications/Skim.app'; # Sage: # http://permalink.gmane.org/gmane.comp.mathematics.sage.support/17166 # glossaries http://tex.stackexchange.com/questions/1226/how-to-make-latexmk-use-makeglossaries add_cus_dep('glo', 'gls', 0, 'makeglo2gls'); sub makeglo2gls { system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo"); } # PythonTeX add_cus_dep('pytxcode', 'pyg', 0, 'pythontexcompile'); sub pythontexcompile { system("pythontex.py $_[0]"); } ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-06 11:25 ` Ken Mankoff @ 2014-05-06 11:40 ` Rainer M Krug 0 siblings, 0 replies; 16+ messages in thread From: Rainer M Krug @ 2014-05-06 11:40 UTC (permalink / raw) To: Ken Mankoff; +Cc: org-mode mailing list, Vikas Rawal, Sharon Kimble [-- Attachment #1: Type: text/plain, Size: 2989 bytes --] Ken Mankoff <mankoff@gmail.com> writes: > On 2014-05-06 at 03:33, Rainer M Krug wrote: >> Ken Mankoff <mankoff@gmail.com> writes: >>> I've found "latexmk" to be the best tool for compiling LaTeX >>> documents. >> >> This sounds very interesting. Could you please provide some details on >> how you use latexmk? Do you use any special options? > > My ~/.latexmkrc file is below. It appears I have extra functions for > making glossaries and working with PythonTeX. There is plenty of support > for latexmk on TeX.SE > https://tex.stackexchange.com/questions/tagged/latexmk > > Since I turn on preview_continuous_mode in my ~/.latexmkrc, I need to > explicitly turn it off if I am calling latexmk from Org, hence the > "-pvc-" option here: > > (setq org-latex-pdf-process (list "/usr/texbin/latexmk -f -gg -pvc- %f")) > > But as I said, I find I prefer to bring up a terminal in the directory > where I am working, and dedicate it to running 'latexmk' in continuous > monitoring mode. When I want to clean up a project I'll run "latexmk -c > file.tex" to discard all of the temporary files. I have Skim.app or > Preview.app (OS X PDF viewers) open the PDF file. I edit Org files, > export to LaTeX (C-c C-e l l), and then keep working while the PDF > regenerates. Thanks a lot - this gives me some ideas on how to use it. I also prefer the terminal approach, and I am using it at the moment, but with no additional parameters. Cheers, Rainer > > -k. > > > > # BEGIN ~/.latexmkrc > > $pdf_mode = 1; > $preview_continuous_mode = 1; > $new_viewer_always = 1; > $silent = 1; # don't stop on errors > $verbose = 0; > #$halt_on_error = 1; > > $clean_ext = 'bbl run.xml %R-blx.bib acn glo xdy synctex.gz'; > > # continue past errors > $force_mode = 1; > $shell_escape = 1; > > # shell escape > $pdflatex = 'pdflatex --shell-escape -file-line-error -synctex=1 %O %S'; > > # $pdf_previewer = 'open -a /Applications/Preview.app'; > $pdf_previewer = 'open -a /Users/mankoff/local/Applications/Skim.app'; > > # Sage: > # http://permalink.gmane.org/gmane.comp.mathematics.sage.support/17166 > > # glossaries http://tex.stackexchange.com/questions/1226/how-to-make-latexmk-use-makeglossaries > add_cus_dep('glo', 'gls', 0, 'makeglo2gls'); > sub makeglo2gls { > system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo"); > } > > # PythonTeX > add_cus_dep('pytxcode', 'pyg', 0, 'pythontexcompile'); > sub pythontexcompile { > system("pythontex.py $_[0]"); > } > > -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer@krugs.de Skype: RMkrug PGP: 0x0F52F982 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! SOLVED. 2014-05-05 23:39 ` John Hendy 2014-05-05 23:51 ` Ken Mankoff @ 2014-05-06 14:13 ` Sharon Kimble 1 sibling, 0 replies; 16+ messages in thread From: Sharon Kimble @ 2014-05-06 14:13 UTC (permalink / raw) To: John Hendy; +Cc: org-mode mailing list, Vikas Rawal [-- Attachment #1: Type: text/plain, Size: 6326 bytes --] John. Thank you for a most informative and useful post. Using your method I've just created the "cat.org" with 14 bibliographic records! I've amended it slightly, which I'll document in line. John Hendy <jw.hendy@gmail.com> writes: > On Mon, May 5, 2014 at 5:23 PM, Sharon Kimble > <boudiccas@skimble.plus.com> wrote: >> Eric S Fraga <e.fraga@ucl.ac.uk> writes: >> > > [...] > >>> >>>> and this is the bibliography file >>>> @Article{, >>> >>> change this line to >>> >>> @Article{1, >>> >>> although I would recommend a more description label personally... >> >> I've set it up with the articles author and year, but it is still >> failing. I'm attaching the original org file, the generated tex and >> pdf, and the bib file. Hopefully this will help find a solution? > > I've been following this from a distance, as I'm interested in > eventually getting into this. I would kindly ask that you slow down > your pace, check things over, and proceed *simply* to solve your > problem. Eric advocated using @Article{1, ... > > Without ever having used biblatex, I immediately wondered whether a > comma delimited bibliography would tolerate: > > @Article{MacRae K, et al;2002, ... > > The answer is that it will not. You also have multiple lines loading > the same package: > > #+LaTeX_HEADER: \usepackage{biblatex} > #+LATEX_HEADER: > \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex} > # #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{biblatex} > > Lastly, I would highly suggest limiting your requests for help to > extremely simple examples. For example, remove packages that do not > affect the behavior of the problem, such as bussproofs, babel, > fancyhdr, etc. > > I was able to get your file working via the following method: > > - Modified cat.bib: > > @Article{1, > author = {MacRae K. Pattison J.}, > title = {Home chemotherapy.}, > journaltitle = {Nursing Times}, > year = {2002}, > key = {1}, > volume = {98}, > number = {35}, > pages = {34-35}, > } > > - Modified/shortened/simplified cat.org: > > # -*- mode:org; mode:reftex; indent-tabs-mode:nil; tab-width:2 -*- > #+OPTIONS: toc:nil num:nil ^:{} > #+TITLE: Cat on the mat - 2014 > #+AUTHOR: Sharon Kimble & Sarah ? > #+LATEX_CLASS: article > #+LATEX_CLASS_OPTIONS: [a4paper] > #+LaTeX_HEADER: \usepackage[backend=biber,style=verbose,style=numeric]{biblatex} > #+LaTeX_HEADER: \bibliography{/home/jwhendy/Downloads/cat.bib} %%% <- > change this path > #+LaTeX_HEADER: \bibliography{cat > > > * Chapter 1 > Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy > nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat.\cite{1} > > * Bibliography > \printbibliography > > Note that you needed to load biblatex before your bibliography (which > you sort of did, but then re-loaded it with a bunch of options and > then perhaps again at the end depending on how Org deals with the # > symbol before #+ lines. You can tweak the options to biblatex however > you'd like; I just simplified a bit to single down to one line loading > it. > > \bibliography needed to call the file cat, not bibliography. > > In addition, I had to run C-c C-e l p to export to latex, then check > the buffer *Org PDF LaTeX Output* for messages regarding the failed > citation. It suggested to run biber on the file cat, which I did from > the command line. > When you add references to "cat.bib" you have to run C-c C-e l p again to generate "cat.blg". > # note that I saved all your stuff in my download folder > $ cd ~/Downloads > $ biber cat > > Make sure you have the biber executable installed. I didn't know > anything about it and thought biblatex might provide it. I had to > explicitly install biber. You should be a path as the response to the > following if you have it: > > $ which biber > > Running biber generated .bbl. Then run "biber cat" on the command line to generate "cat.bbl". Then you can run "C-c C-e l p" on "cat.org" which generates "cat.pdf" which includes the bibliography! Yahay! Success! > > Then, re-running C-c C-e l p from Org works for me (at least I think; > see attached to verify). > > Lastly, when I encountered an error, I googled to find out what to do: > - Using biber: http://tex.stackexchange.com/questions/26516/how-to-use-biber > - Why \bibliography was giving me an error: > http://kb.mit.edu/confluence/pages/viewpage.action?pageId=3907111 > > If this works, someone can chime in regarding how to modify Org so > that it will run the necessary biber/biblatex commands so you don't > have to jump to a command line every time. Or perhaps that's a one > time thing -- maybe as long as biber generates the .bbl file, you can > refer to anything you want in that file from then on? If you have this in your ".emacs" --8<---------------cut here---------------start------------->8--- ;; 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" "biber %b" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f" "xelatex -shell-escape -interaction nonstopmode -output-directory %o %f")) --8<---------------cut here---------------end--------------->8--- it will generate the file "cat.bbl" and include the bibliography in the pdf, without you having to run "biber" from the command-line. You still need to keep an eye on "*Org PDF LaTeX Output*" as it is here where it lists any errors it finds, and what its done and what it recommends you to do. And I have just generated a complete working "foo.bbl" for my book that I'm writing using the above code without calling "biber" from the command-line. It works! > > Hope that helps, > John > Yes, John, it very much does. It all works now! Sharon. -- A taste of linux = http://www.sharons.org.uk my git repo = https://bitbucket.org/boudiccas/dots TGmeds = http://www.tgmeds.org.uk Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 818 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* Re: Bibliography woes! 2014-05-05 22:23 ` Sharon Kimble 2014-05-05 23:39 ` John Hendy @ 2014-05-05 23:47 ` Leonard Avery Randall 1 sibling, 0 replies; 16+ messages in thread From: Leonard Avery Randall @ 2014-05-05 23:47 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode mailing list, Vikas Rawal [-- Attachment #1: Type: text/plain, Size: 386 bytes --] Hi, As Henry just noted, one of your main problem is your bibtex key. It should not contain spaces, commas, backslashes, semicolons, or other special characters that might mess up the syntax of the bibtex file. A common convention is to use author:year or if you have many articles by the same authors in the same year you can use author:yeara, author:yearb etc. All best, Leonard [-- Attachment #2: Type: text/html, Size: 693 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
end of thread, other threads:[~2014-05-06 14:13 UTC | newest] Thread overview: 16+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2014-05-05 12:05 Bibliography woes! Sharon Kimble 2014-05-05 12:26 ` Vikas Rawal 2014-05-05 12:33 ` Leonard Avery Randall 2014-05-05 14:45 ` Sharon Kimble 2014-05-05 15:07 ` Vikas Rawal 2014-05-05 15:48 ` Leonard Avery Randall 2014-05-05 17:08 ` Sharon Kimble 2014-05-05 18:26 ` Eric S Fraga 2014-05-05 22:23 ` Sharon Kimble 2014-05-05 23:39 ` John Hendy 2014-05-05 23:51 ` Ken Mankoff 2014-05-06 7:33 ` Rainer M Krug 2014-05-06 11:25 ` Ken Mankoff 2014-05-06 11:40 ` Rainer M Krug 2014-05-06 14:13 ` Bibliography woes! SOLVED Sharon Kimble 2014-05-05 23:47 ` Bibliography woes! Leonard Avery Randall
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