Hi Michael,
It took me a while to isolate the problem: it's displayed math in Chapter03 that causes it. This turned out to be a bug in the package ulem:
http://tex.stackexchange.com/questions/125980/problem-with-amsmathfontspeculem
http://tex.stackexchange.com/questions/120024/pdflatex-hangs-with-no-errors


In short, the way ulem defines MakeRobust makes amsmath enter an infinite loop.


There are a few fixes, I'll give you two:

- either call fixltx2e in classicthesis-config.tex before the call to amsmath (CUT & PASTE ABOVE)

- or add te following to ClassicThesis.lyx (main document), Document Settings > Local Layout

Provides ulem 1
AddToPreamble
  \usepackage{ulem}
EndPreamble

(don't forget to Validate before pressing Apply)
to make sure ulem is loaded after amsmath.


Let me know if this worked.


LyX calls the two packages in the right order (intentionally or not). Unfortunately, the LyX port of the classic thesis template is a bit messy as the author of the latex template insisted on keeping many unnecessary calls in classicthesis-config.tex

















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