Someone compiled a simple test file with the following result, so there might be a packaging issue with the logo PDF:
This is XeTeX, Version 3.14159265-2.6-0.99991 (TeX Live 2014) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
(./sample-book.tex
LaTeX2e <2014/05/01>
Babel <3.9k> and hyphenation patterns for 78 languages loaded.
(./tufte-book.cls
Document Class: tufte-book 2010/03/28 v3.5.1 Tufte-book class
(./tufte-common.def0
...
(/usr/local/texlive/2014/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/local/texlive/2014/texmf-dist/tex/latex/tools/multicol.sty)))
(/usr/local/texlive/2014/texmf-dist/tex/lualatex/lilyglyphs/lilyglyphs.sty
(/usr/local/texlive/2014/texmf-dist/tex/latex/pgf/basiclayer/pgf.sty
(/usr/local/texlive/2014/texmf-dist/tex/latex/pgf/utilities/pgfrcs.sty
...
Package hyperref Warning: Rerun to get /PageLabels entry.
ABD: EverySelectfont initializing macros
*geometry* driver: auto-detecting
*geometry* detected driver: xetex
ABD: EveryShipout initializing macros
LaTeX Warning: File `lilyglyphs_logo.pdf' not found on input line 6.
./sample-book.tex:6: Unable to load picture or PDF file 'lilyglyphs_logo.pdf'.
<to be read again>
}
l.6
?
<use "lilyglyphs_logo.pdf" >
./sample-book.tex:6: Unable to load picture or PDF file 'lilyglyphs_logo.pdf'.
<to be read again>
\GXT@clipend
l.6
?
<use "lily-crescHairpin.pdf" >
Package bibentry Warning: You have used \nobibliography*
(bibentry) without a following \bibliography.
(bibentry) You may not be able to run BibTeX.
[1] (./sample-book.aux)
)
Output written on sample-book.pdf (1 page).
SyncTeX written on sample-book.synctex.gz.
Transcript written on sample-book.log.
Someone compiled a simple test file with the following result, so there might be a packaging issue with the logo PDF: