# \ref and \cite stopped working

My WinEdt version had to be reinstalled and now I can't use PDFTexify or Texify. That wouldn't be a problem since I still can use PDFLaTeX. So I try that, what happens? Now, all \cite{} show [?] and \ref{fig:} and \ref{tab:} show ?. And I dont even get a TOC! Some example from thesis.tex:

\include{./preamble}
\begin{document}
\tableofcontents
\include{./chapter1}
\include{./bibliography}
\end{document}


The preamble:

\documentclass[12pt,a4paper]{report}
\usepackage[swedish,english]{babel}
\usepackage[T1]{fontenc}
\usepackage[ansinew]{inputenc}
\usepackage[a4paper,
top    = 2.5cm,
bottom = 2.5cm,
left   = 2.5cm,
right  =2.5cm]{geometry}
\usepackage{float, wrapfig, times, graphicx, amsmath, multirow,  sidecap,longtable,color, soul, threeparttable, mathtools, amssymb}
\usepackage[toc,page]{appendix}
\setlength{\textfloatsep}{0cm} \setlength{\floatsep}{0cm}
\setlength{\intextsep}{0.4cm}
\AtBeginDocument{%
\captionsenglish % Captions in english
\dateenglish     % Date format in english
}
\widowpenalty=10000
\clubpenalty=10000
\newcommand{\HRule}{\rule{\linewidth}{0.3mm}}


The .bib file:

\begin{thebibliography}{99}
\bibitem{}
\end{thebibliography}


chapter 1

just text


The funny thing is, if I put the whole bibliography in the bottom of thesis.tex, the \cite{} works fine.

Btw. First of all, I would love to have texify work without any problems but if you don't know how to fix that, I'd still love it if you could help me with the referencing. Oh, and the TOC, too.

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pdflatex needs at least two runs to get cross-references right. You probably need to set up the quick compilation configs to get the right number of runs (sorry, I'm not a windows user) –  henrique Oct 6 '12 at 14:08

As far as I remember, you have to run pdflatex twice, then bibtex (or biber), and then pdflatex at least one more time.

If the texify you refer to is miktex-texify, normally, miktex binary folder is in the path on a windows-machine. Therefore, you can run texify from the command-line.

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First of all with your code snippets we can't proof what is happening or not. We need a complete minimal working example (MWE). To include an short example of your used bib file please use package filecontents (texdoc filecontents for the manual) to include it in one MWE.

Do you use bibtex or biber for your bibliography? I assume bibtex for the following.

If you have problems with your editor first check whether you can compile your MWE from the command line. Change to the directory that contains your MWE, for example c:\test\mwe.tex and try pdflatex mwe.tex. This creates the aux file you need (proof it). Now use bibtex mwe (or bibtex8 mwe) to create the bibliography. Now run pdflatex mwe twice, better three times to create all cross references, the correct table of contents and the bibliography.

If this is compiling well, you have to configure your new editor WinEdt (version 7?) new. In this case please have a look into the manual.

If not, you have a problem with your TeX installation.

MiKTeX's texify runs pdflatex and bibtex (not biber!) as needed to get a final document. In WinEDT version 7 you can start this kind of compiling using TeX-> TeXify. If that does not work, try to uninstall WinEDT and install it new and give WinEDT a chance to recognize that MiKTeX is installed. You can test if texify is working with texify mwe in your command line.

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I see now that when I create a new file, everything seem to work. I guess the problem was that I pasted all the old .tex files in a different folder (backup). Then I erased all the files in the old folder (all, .aux, .bak etc). When I now moved them .tex files back, texify cant find any .aux files. But I dont understand why it doesnt create new ones? I have also tried copying the content of an old file into a new document, this works!(if I name the new file e.g. thesis2 instead of thesis). Then I just have to run texify and the .aux files are created (with wrong names, e.g. chapter1.2.aux) –  Anders Kallenberg Oct 7 '12 at 8:44
Everything works fine again, thank u for your time though. I just had to compile the files using new names and then change back on both .tex and .aux. BTW I have never used bibtex, not deliberately. I have all my references in a .tex file that begins with \begin{thebibliography} \bibitem{name} Author. Title. Publisher.year.\\\bibitem{newname}...All problems began when I wanted to sort that bibliography, cause its tedious sorting by hand in the file –  Anders Kallenberg Oct 7 '12 at 8:59
I suggest you use BibTeX or better biblatex and biber to build your bibliography. Sorting is then no problem! If you use \include{chapter1} you will get a file chapter1.aux. That is okay. –  Kurt Oct 7 '12 at 14:28