Lilypond-Book error

[S L Raymond]

I'm running lilypond-book 2.6.3.  I tested an article containing
lilypond code according to the instructions at
http://lilypond.org/doc/v2.6/Documentation/user/lilypond/An-example-of-a-musicological-document.html#An-example-of-a-musicological-document
 ,
and it worked fine.  Then, however, I ran the program using a more
complex document -- a book, containing a chapter which in turn contained
the code snippet, and this is what I get:

lilypond-book: error: Output would overwrite input file; use --output.

What can be done?

Lyle