[Tex/LaTex] How to re-run Bibtex on the file(s) – RSweave; KnitR

biblatexknitrmarkdownrnwsweave

I have a document called Code.Rnw where I write my document in and I'm using Sweave and Knitr to compile it.

For my bibliography I use biblatex. My setting is the following:

\usepackage[bibstyle=authoryear, citestyle=authoryear, backend=bibtex8]{biblatex}
\bibliography{bib}

Unfortunately my whole header is very long so I won't post it.

Until now the bibliography file (bib.bib) was printed in the PDF output without any problems but suddenly the following error occured:

Please (re)run Bibtex on the file(s):(biblatex) Code(biblatex) and rerun Latex afterwards.

Actually I don't have a clue how to (re)run Bibtex especially in the environment with Sweave and KnitR. I can't run my bib file or any other file seperatly; except for my main Rnw (Code.Rnw) file of course. How do I deal with the situation?

Thanks

Best Answer

For anyone having a similar problem. I found, that my Code.BBL file wasn't updating anymore when I compiled the document. For now the solution is the following: Update the bibliography file (in my case bib.bib) and save it. Delete the Code.BBL file (yours will have the name of your Rnw document) and then compile the Code.Rnw (or whatever your main document is named) 2 times. This creates a PDF output for me.

Related Solutions

[Tex/LaTex] BibTeX works, but not biblatex

The following MWE (including your bib file, a few minor changes to yours) should run on your system without errors and only one correct warning: overwriting file \jobname.bib (that tells you that file \jobname.bib has been rewritten. \jobname is changend to the name of your texfile. for example test. You have to run: pdflatex test.tex, bibtex test, pdflatex test.tex, pdflatex test.tex).

%http://tex.stackexchange.com/questions/83128/bibtex-works-but-not-biblatex
\RequirePackage{filecontents}
\begin{filecontents*}{\jobname.bib}
@BOOK{KandR,
  AUTHOR    = {Kernighan, Brian W. and Ritchie, Dennis M.},
  TITLE     = {{The C Programming Language Second Edition}},
  PUBLISHER = {Prentice-Hall, Inc.},
  YEAR      = {1988},
}
\end{filecontents*}

\documentclass{article} 
\usepackage[%
  backend=bibtex   % use BibTeX
% backend=biber    % Use biber
]{biblatex} 
\addbibresource{\jobname.bib}
\begin{document} 
Hello \cite{KandR}. How are you?
\printbibliography 
\end{document}

[Tex/LaTex] Citing (author, journalabbr., year) needed

First thing to do is to add a field for the journal abbreviation to the article entrytype, journalabbr in the MWE. Therefore you need to declare a datamodel (an extra file; in the MWE I've used filecontents to simulate that) and you have to tell biblatex/biber to use it in the package options.

Then you have to modify the cite command, so it fits your needs. \citep from the authoryear-style (your citestyle) uses the \cite command. There you just have to add a switch, which checks if the field journalabbr is empty or not, and prints it out or not.

Last but not least you have to add the abbreviation fields to the entries.

MWE:

\begin{filecontents}{min.bib}
@article{boisson2003unexpected,
  title={Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote},
  author={Boisson, B. and Giglione, Carmela and Meinnel, Thierry},
  journal={Journal of Biological Chemistry},
  journalabbr={JBC},
  year={2003},
  publisher={ASBMB}
}
\end{filecontents}

\begin{filecontents}{authorjabbryear.dbx}
\ProvidesFile{authorjabbryear.dbx}
\DeclareDatamodelFields[type=field,datatype=literal]{journalabbr}
\DeclareDatamodelEntryfields[article]{journalabbr}
\end{filecontents}

\documentclass[fontsize=11pt, paper=a4, ngerman, DIV=calc]{scrartcl}
\usepackage[scaled]{helvet}
\renewcommand*\familydefault{\sfdefault}
\usepackage{fixltx2e}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{babel}
\usepackage[german=quotes]{csquotes}
\usepackage[style=authoryear-comp,sortcites=true,sorting=nyt,isbn=false,natbib=true, citestyle=authoryear,bibstyle=authoryear,backend=biber,maxnames=1,maxcitenames=1,
,datamodel=authorjabbryear%added!
] {biblatex}

\DefineBibliographyStrings{ngerman}{ andothers = {{et\,al\adddot}} }

\renewbibmacro*{cite}{%from authoryear.cbx
  \iffieldundef{shorthand}
    {\ifthenelse{\ifnameundef{labelname}\OR\iffieldundef{labelyear}}
       {\usebibmacro{cite:label}%
        \setunit{\addspace}}
       {\printnames{labelname}%
        \setunit{\nameyeardelim}}%
     \iffieldundef{journalabbr}{}{%
        \printfield{journalabbr}%
        \setunit{\nameyeardelim}%
        }%
     \usebibmacro{cite:labelyear+extrayear}}
    {\usebibmacro{cite:shorthand}}}

\addbibresource{min.bib}

\begin{document}

\citep{boisson2003unexpected} 

How it should look like: 

(Boisson et al., JBC, 2003)

\printbibliography

\end{document}

Best Answer

Related Solutions

[Tex/LaTex] BibTeX works, but not biblatex

[Tex/LaTex] Citing (author, journalabbr., year) needed

Related Question