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SOLVED

The cause of the problem was the include(s) at top of my main tex file, i changed them to input and now it works.

I've read the documentation of the glossary package and a lot of examples (g.e. this, or this), but my glossary items will be referenced, the glossary itself otherwise won't be printed. All the other indexes/toc are working. Has someone an idea?

Minimal working example:

\documentclass{scrreprt}
\usepackage[toc,acronym]{glossaries} 

\makeglossaries

\newglossaryentry{bar}{name={bar}, description={\ldots}}
\newglossaryentry{baz}{name={baz},description={\ldots}}

\newacronym{foobar}{foobar}{\ldots}

\begin{document}
\section{foo section}
Lorem ipsum \gls{bar} \gls{baz} and \gls{foobar}.

\printglossary[type=main,title={Glossary},toctitle={Glossary}]
\thispagestyle{empty}\cleardoublepage
\printglossary[type=\acronymtype,title={List of Abbreviations},toctitle={List of Abbreviations}]

\end{document}

Below the one that makes problems:

Makefile:

all:
xelatex thesis
biber thesis
makeglossaries thesis
xelatex thesis

thesis.tex

\RequirePackage[l2tabu, orthodox]{nag}
\documentclass[a4paper]{scrreprt}

\include{header/header}
\include{header/commands}
\include{header/settings}

\makeglossaries
\bibliography{bibliography/thesisbib}

\include{appendix/glossary}

\begin{document}
\input{variables/global}

\pagenumbering{roman}
\begin{titlepage}
    \input{frontpage/frontpage}
\end{titlepage}
\newpage
\input{frontpage/title_backside}
\newpage

{
    \onehalfspacing
    \input{abstract}
}
\blankpage{\thesisBlankPageText}

\tableofcontents
\blankpage{\thesisBlankPageText}

\pagenumbering{arabic}
\chapter{foo}    
\section{bar}    
\gls{computer} is a machine and \gls{mah}, \gls{aca}.
\blankpage

\appendix 
\pagenumbering{Alph}

\cleardoublepage
%\addcontentsline{toc}{subsection}{Glossar}
\glsaddall
\printglossary[type=main,title={Glossary},toctitle={Glossary}]

\addcontentsline{toc}{chapter}{\listfigurename}
\listoffigures
\addcontentsline{toc}{chapter}{\listtablename}
\listoftables
\addcontentsline{toc}{chapter}{\bibname}
\input{bibliography/bibliography}
\end{document}

glossary.tex:

\newglossaryentry{computer}
{
  name=computer,
  description={\ldots}
}
\newglossaryentry{mah}
{
  name=mah,
  description={\ldots}
}
\newacronym{aca}{aca}{a contrived acronym}
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closed as too localized by tohecz, egreg, Claudio Fiandrino, mafp, Torbjørn T. Jun 1 '13 at 11:18

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You should provide a compilable example, so that one can reproduce your issue. –  karlkoeller May 31 '13 at 15:32
    
What are all those \includes doing in the preamble? If they are files containing 'personal' commands and so forth, you should name them .sty and load them as normal packages \usepackage. (Note this is not likely the source of your problem, but it is impossible to tell since we don't know what's in them. If they are not related to the problem, you should remove them from a minimal(!) example; and if they are related, then you need to elaborate on their contents.) –  jon May 31 '13 at 16:30
    
It also looks like you are calling your bibliography twice..? –  jon May 31 '13 at 16:31
1  
@jon Using \input is perfectly fine; surely \include is out of place in the preamble. –  egreg May 31 '13 at 16:40
1  
Does makeglossaries produce any error messages? Are there any errors in the glossary log files (.glg etc)? –  Nicola Talbot May 31 '13 at 17:20
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