I am using xelatex and I have the following warnings:

!!!** WARNING ** Annotation out of page boundary.!!!
!!!** WARNING ** Current page's MediaBox: [0 0 597.6 842.4]!!!
!!!** WARNING ** Annotation: [303.194 712.675 612.035 728.575]!!!
!!!** WARNING ** Maybe incorrect paper size specified.!!!

All answers that I have found in the Internet don't work for me. They does not change anything, provide errors.

I have discovered that when I remove

\setmainfont{Times New Roman}

this problem dissapears.

\documentclass[a4paper, 12pt]{article}

\usepackage[top=0.5in, bottom=1.0in, left=0.8in, right=0.8in, includehead, includefoot]{geometry}
\usepackage{enumitem}        % configure lists


\usepackage{commath}        % \dif sign


\setmainfont{Times New Roman}


\section{Implementation and results}
% Implementation and results {{{
% -----------------------------------------------------------------------------
The implementation is one-dimensional Euler equations simulation using Roe
solver written in C++.
The code is located in a public git \cite{Git} repository, url:
Compilation prerequisites and instructions could be found in the
\textit{``ReadMe.md''} file.

OpenCl \cite{OpenCl} is used for the problem computations. Changes to the
solver as well as boundary conditions and initialization data could be applied
without recompilation of the application by modifying \textit{``Kernel.cl''},
which is an OpenCl file.

The boundary conditions are \textit{solid walls} that the fluid reflects at
this boundaries in a particular way,
  p_{0} &= p_{1}, \nonumber \\
  {\rho}_{0} &= {\rho}_{1}, \\
  u_{0} &= -u_{1} \nonumber
for the left boundary. The same approach is applied for the right one.

% References {{{
% -----------------------------------------------------------------------------
  \bibitem{LeVeque} R.J. LeVeque, \emph{Finite Volume Methods for Hyperbolic
    Problems}, vol. 31, Cambridge University Press, 2002.
  \bibitem{Anderson} John D. Anderson, Jr., \emph{Computational Fluid Dynamics,
    The basics with applications}, 1995.
  \bibitem{Git} \emph{Git manual page}, URL: \url{http://gitmanual.org/}.
  \bibitem{OpenCl} \emph{The open standard for parallel programming of
  heterogeneous systems}, URL: \url{http://www.khronos.org/opencl/}.
% -----------------------------------------------------------------------------
% References }}}




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The font change was only accidentally related, the warning was telling you that the link was off page, changing the font just changed the paragraph setting so that the link could break at a / You can add - to the list of URL break characters then things work out as shown:


\setmainfont{Times New Roman}

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