* 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
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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
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^ 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
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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
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^ 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
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>
> 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
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* 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
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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
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^ 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
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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.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/xelatex/xetex-def/xetex.def)))
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(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rotating/rotating.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
Package hyperref Message: Driver (autodetected): hxetex.
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(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
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*
* OpenType feature 'Numbers=Monospaced,Lining' (+tnum) not available for font
* 'LinLibertine_RZI' with script 'Latin' and language 'Default'.
*************************************************
*************************************************
* fontspec warning: "icu-feature-not-exist-in-font"
*
* OpenType feature 'Numbers=Monospaced,Lining' (+tnum) not available for font
* 'LinLibertine_RZI' with script 'Latin' and language 'Default'.
*************************************************
(/usr/share/texlive/texmf-dist/tex/latex/libertine/LinLibertine_R.tex)
(/usr/share/texlive/texmf-dist/tex/latex/libertine/LinBiolinum_R.tex)
(/usr/share/texlive/texmf-dist/tex/latex/libertine/LinBiolinum_K.tex)
(/usr/share/texlive/texmf-dist/tex/latex/libertine/LinLibertine_I.tex)
(/usr/share/texlive/texmf-dist/tex/latex/libertine/LKey.tex))
(/usr/share/texlive/texmf-dist/tex/latex/xltxtra/xltxtra.sty
(/usr/share/texlive/texmf-dist/tex/latex/realscripts/realscripts.sty
*************************************************
* LaTeX warning: "xparse/redefine-command"
*
* Redefining document command \textsubscript with arg. spec. 's' on line 25.
*************************************************
*************************************************
* LaTeX warning: "xparse/redefine-command"
*
* Redefining document command \textsuperscript with arg. spec. 's' on line 28.
*************************************************
) (/usr/share/texlive/texmf-dist/tex/latex/metalogo/metalogo.sty))
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.sty
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex2.sty
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/logreq/logreq.sty
(/usr/share/texlive/texmf-dist/tex/latex/logreq/logreq.def))
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/blx-dm.def)
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/blx-compat.def)
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.def)
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/blx-natbib.def)
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/bbx/standard.bbx))
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/cbx/authoryear-icomp.cbx)
(/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/bussproofs/bussproofs.sty
Proof Tree (bussproofs) style macros. 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
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^ 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
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^ 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
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^ 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
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^ 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 --]
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^ 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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