The newest versions of the package xy-pic does not work properly with LuaLaTeX, version 0.95.0. Consider the following simple example:
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{fontspec}
\usepackage[all]{xy}
\begin{document}
\[
\xymatrix {
A\ar[r]\ar[d] & B\ar[d]\\
C\ar[r] & D
}
\]
\end{document}
The first error message, which appears while compiling this with lualatex is
Package xypdf Error: pdfTeX version 1.40.0 or higher is needed for the xypdf
It’s possible to avoid this error message by adding the following line at the beginning of /usr/share/texlive/texmf-dist/tex/generic/xypic/xypdf.tex
\input /usr/share/texmf/tex/generic/context/luatex/luatex-pdf.tex
However, even then LuaLaTeX produces errors:
ERROR: Undefined control sequence.
\line@ ->\setboxz@h {\xP@setsolidpat \xP@stroke
{0 0 m \xP@coor {\cosDirecti...
l.13 }
and the result looks like this:



tikz-cd, IMO it ends up looking better and is more flexible. – daleif Sep 08 '16 at 14:57\input{luatex-pdf}immediately after the\documentclassline. And don't modify distributed files. – egreg Sep 08 '16 at 15:05