Comment #52 on issue 2533 by [email protected]: Patch: line_count fixes http://code.google.com/p/lilypond/issues/detail?id=2533
As I wrote in comment #48: try ./configure --disable-optimising before make all, and then run the exexutable on input/regression/repeat-sign.ly. You only get assertion checks for --disable-optimising (what I consider a design error), so if you want to debug this, you need to recompile with that option.
