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I have created a project within TexLipse and right before the end of the document I use the command \bibliography{bibtexfile} \bibliographystyle{plain} to create the bibtex reference section. However, when I build my project in TexLipse, the reference section does not show. Also selecting "Run BibTex on next build" does not have any effect.

If I move \bibliography{bibtexfile} \bibliographystyle{plain} to the line after \maketitle, the section is created. But I want the section at the end of my document, not the beginning.

If I use a different editor, like TexMaker, and do: pdflatex, bibtex, pdflatex, pdflatex, everything works fine. It seems like TexLipse does not run bibtex at all.

Even with a .bat file everything works fine:

pdflatex main.tex  
bibtex main.aux  
pdflatex main.tex  
pdflatex main.tex

What could be the problem?

OK! Seems like I fixed it myself
I use \input{} to include external files, but apparently TexLipse does not like it when the commands \bibliography{bibtexfile} \bibliographystyle{plain} are externally called. TexLipse wants them in the main tex file.

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closed as too localized by Mico, egreg, lockstep, Torbjørn T., topskip Apr 7 '12 at 8:30

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did you also define a \bibliographystyle{}? Did you use \cite{key} in the document or \nocite{*} to output all references? What happens if you run bibtex from the command line? – Martin H Mar 14 '12 at 11:52
Yes I use the \bibliographystyle{} command and also \cite{key}. It all works fine when I do it with texmaker, with command line or even with a bat file: pdflatex main.tex bibtex main.aux pdflatex main.tex pdflatex main.tex (6 references are created). Even weirder: when I put the \bibliography{bibtexfile} \bibliographystyle{plain} after \maketitle, TexLipse creates the references without a problem. – ohokke Mar 14 '12 at 12:03
Disagree with the closing... this is a very useful question. – KDN Sep 17 '12 at 15:12
Diasgree with closing. This is applicable to anybody using TeXlipse. (and I have the same problem right now ;)) – Simon W Dec 29 '13 at 12:39
Running "Project -> Clean..." sometimes helps if TeXlipse/BibTeX are not working properly. – ShinNoNoir Jan 3 '14 at 13:01

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