You said that if you use File->Export->LaTeX and then run pdflatex manually, the document compiles correctly (nothing hangs), right? If so, then it shouldn't be the class file, because the same class file is being used in the manual run. If I'm wrong about exporting to LaTeX working, then that suggests either the class file or the document itself has something funny in it.

Compiling the document manually works very well, in my case I do
- pdflatex example.tex
- bibtex example
- pdflatex example.tex
- pdflatex example.tex
and it finishes successfully.

If pdflatex is hanging while scanning the auxiliary file, it could be that the file is terminated incorrectly (so that pdflatex is waiting for more input), or it could be that something has a lock on the file (and pdflatex is waiting to begin reading it).

This might be possible, but how to debug?
In a posting from the texlipse mailing list I read about texify. So I replaced the pdflatex.exe command in LyX with texify.exe plus additional parameters for pdf generation and then I could export my LyX documents to pdf. And there were no errors...

Do you have labels and cross-references in the document? IIRC, the .aux file is also used for cross-references, not just citations. I'm not sure what one could do with a cross-reference that would cause pdflatex to hang -- missing labels would not cause that -- but perhaps if a label contains a non-latin character it might cause a problem. (I'm groping in a very dark place here.)

No, but the .aux file contains some data about footnotes (in my document class I use the footmisc package) as well as citation data.

/Paul

Thanks...

Florian

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