How to check conflicts happening between packages

Question

I am not sure whether there are many people having the same problem with me or not. The thesis includes several of the .tex files as chapters, sections, parts, etc. Now I would like to refine or add some features, I need to load correct packages. But I do not know exactly which the packages loaded already some similar features. I have read a tip that it should add \usepackage{etex}\reserveinserts{28} in the preamble. So my question is How to check and verify which packages are needed to load first others?
For example, below is the collection of packages I am using for my thesis.

%% Language %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{etex}
\reserveinserts{28}
\usepackage[english]{babel} %francais, polish, spanish, ...
\usepackage[T1]{fontenc}
\usepackage[utf8x]{inputenc}
\usepackage{multido}
\usepackage{lmodern} %Type1-font for non-English texts and characters
\usepackage[a4paper]{geometry}
\usepackage{helvet}

%% Packages for Graphics & Figures %%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[pdftex]{graphicx}   %%For loading graphic files
\usepackage{subfig}         %%Sub-figures inside a figure
\usepackage{pdflscape}
\usepackage{wrapfig}
\usepackage{tikz}       %%Generate vector graphics from within LaTeX
\graphicspath{{images/}}    %%Define a source folder of images

%% Math Packages %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{bpchem}
\usepackage{nth}
\usepackage{amsmath}
\numberwithin{equation}{section}
\usepackage{amsthm}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{caption}
\usepackage{sansmath} %% For inserting math formulas into captions //// Notes
\usepackage[algo2e,slide,boxruled,vlined,linesnumbered,algosection]{algorithm2e}
%% Using the option algochapter: algorithms are numbered within chapter numbers.
%% Dung goi nay thi khong can add bang tay cac muc
% \newcommand{\listofalgorithms}{\tocfile{\listalgorithmcfname}{loa}}
% \newlistof{listofalgorithms}{loa}{\listalgorithmcfname}
% \newcommand{\listofalgorithmes}{\tocfile{\listalgorithmcfname}{loa}}
\usepackage{algpseudocode}

%% Other Packages %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{a4wide}   % Smaller margins = more text per page.
\usepackage{fancyhdr} % Fancy headings
\usepackage[sectionbib]{chapterbib}
\usepackage{paralist}
\usepackage{url}
\usepackage{array}
\usepackage{rotating}
\usepackage{ucs}
\usepackage[numbers,square,comma,sort&compress]{natbib}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage{pdflscape} %better
\usepackage{colortbl}
\newcommand{\mc}[2]{\multicolumn{#1}{c}{#2}}
\usepackage[dvipsnames]{xcolor}
\usepackage{color}
\usepackage{eqparbox}

\usepackage[breakable]{tcolorbox}

 \usepackage{blindtext}
 \tcbuselibrary{skins,breakable}

 \usepackage{enumerate}

\renewcommand*{\bibnumfmt}[1]{\eqparbox[t]{bblnm}{[#1]}}
\usepackage{pdfpages} %% Pour Include pdf files
\usepackage{makeidx}
\usepackage[explicit]{titlesec}
\usepackage[Lenny]{fncychap}
\usepackage[tight]{minitoc}
\usepackage{titletoc}
\usepackage[subfigure]{tocloft}
\renewcommand{\cftsecfont}{\normalfont} 
\usepackage[backref=page]{hyperref} %% [pagebackref] or [backref=page]
\def\backref#1{{\scriptsize [#1]}}
\def\theaipage{\string\hyperpage{\thepage}}
\usepackage{cleveref} % using smart citations
\usepackage{listings} % for formatting source codes
\usepackage{pifont}
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%
%% Line Spacing %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{setspace}
%\setstretch{1.3}
%\singlespacing        %% 1-spacing (default)
%\onehalfspacing       %% 1,5-spacing
%\doublespacing        %% 2-spacing

\usepackage{alltt}
% Using quotations
\usepackage{dirtytalk}
\expandafter\def\expandafter\quote\expandafter{\quote\small\singlespacing}
\usepackage{quoting}
\quotingsetup{vskip=0pt}

%%% Using shading in verbatim
\usepackage{fancyvrb, pstcol,framed}
\definecolor{shadecolor}{rgb}{.9, .9, .9}
\definecolor{timberwolf}{rgb}{0.86, 0.84, 0.82}
\usepackage{changepage} % to use adjustwidth for dedication
\usepackage{floatrow} %no need because of using \captionsetup[table]
\usepackage{textpos}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Options / Modifications
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newtheorem{theorem}{Theorem}[chapter]
\newtheorem{thm}{Theorem}[chapter]
\newtheorem{definition}[theorem]{Definition}
\newtheorem{example}[thm]{Example}
\newtheorem{mydef}{Definition}
\newtheorem{proposition}{Proposition}[chapter]

\makeatother
\makeindex

\usepackage[acronym,toc]{glossaries}
\makeglossaries

\definecolor{SpringGreen}{rgb}{0.0, 1.0, 0.5}
\definecolor{TeaGreen}{rgb}{0.82, 0.94, 0.75}
\definecolor{Gray}{gray}{0.85}
\definecolor{LightCyan}{rgb}{0.88,1,1}
\definecolor{darkblue}{RGB}{25,75,112}
\definecolor{brown}{RGB}{102,0,51}
\definecolor{lightblue}{rgb}{.90,.95,.30}
\DeclareCaptionFont{blue}{\color{blue}}
\DeclareCaptionFormat{listing}{\colorbox{gray}{\parbox{\textwidth}{#1#2#3}}}
\DeclareCaptionFormat{table}{\colorbox{red}{\parbox{\textwidth}{#1#2#3}}}
\definecolor{coolblack}{rgb}{0.0, 0.18, 0.39}
\floatsetup[table]{capposition=top} % ISO7144-1986
\captionsetup{
  margin=1cm,
  format=hang,
  font=footnotesize,
  format=plain,
  labelfont={bf,up},
  labelsep=colon,
  width=13cm,
%   indention=10pt
}

\usepackage{soul} % using text highlight
\sethlcolor{lightblue}
\usepackage{tabu}
\captionsetup[lstlisting]{
  format=listing,
  labelfont=white,
  textfont=white
}
\lstset{
         basicstyle=\footnotesize\ttfamily, 
         numbers=left,               
         numberstyle=\tiny,          
         %stepnumber=2,              
         numbersep=10pt,             
         tabsize=1,                  
         extendedchars=true,         
         breaklines=true,            
         keywordstyle=\color{red},
         frame=b,         
         stringstyle=\color{blue}\ttfamily, 
         showspaces=false,           
         showtabs=false,             
         xleftmargin=12pt,
         framexleftmargin=17pt,
         framexrightmargin=5pt,
         framexbottommargin=4pt,
         backgroundcolor=\color{white},
         showstringspaces=false
 }
\hypersetup{
  pdfauthor={NGUYEN Vu Ngoc Tung},
  pdftitle={PhDThesis: Analysis of biochemical reaction graph},
  pdfcreator={NGUYEN Vu Ngoc Tung},
  colorlinks=true,
  citecolor=blue, 
  linkcolor=blue,
  linktoc=all,
  urlcolor=blue
}

The reason I have this question is that if I have asked a question of A lot of unexpected spaces between paragraph after inserting colorbox. I appreciate the answer because the result is really efficient. If I add the packages as suggested in the answer, tex gives the error as below.

! No room for a new \write .
\alloc@ ...else \errmessage {No room for a new #2}
                                                  \fi \fi 
l.161 \listoftables

But I remove those packages, of course tex compile does not understand tcolorbox.
I let here the tex files included in my thesis. Finally, could you have look my project? The files are organized as follows:

thesis.tex
--- packages.tex
--- chapter1.tex
--- chapter2.tex

The following are contents of the files respectively. thesis.tex

\documentclass[a4paper,twoside,openright,12pt]{report}
\input{packages}
\begin{document}
\input{chapter1}
\input{chapter2}
\end{document}

packages.tex It has just mentioned above.

chapter1.tex (for example, not real contents)

\subsection{Determining MCSs}
The MCS algorithm devised by Klamt and Gilles relies on the 
fact that:
\begin{itemize}
 \item any feasible steady state flux distribution in a given network, 
expressed by a vector of the net reaction rates, $r$, can be represented by a 
non-negative linear combination of EFMs as illustrated in 
\Cref{eq:steady-state2} (reused from Klamt2006):
\begin{equation}\label{eq:steady-state2}
 r = \sum_{i=1}^{N}\alpha_{i}E_{i}, (\alpha_{i} \geq 0)
\end{equation}
 \item where $N$ is the number of EFMs.
 \item the removal of reactions from the network results in a new set of EFMs 
constituted by those EFMs that do not involve the deleted reactions.
\end{itemize}
\paragraph{}Before MCSs are computed, the set of $EFMs$ is split into 
two disjoint sets:
\begin{itemize}
 \item the set of target modes ($EFM^t$), i.e., all EFMs ($e^{t,j}$) involving 
the objective reactions $t$.
 \item the set of non-target modes ($EFM^{nt}$), i.e., EFMs not involving the 
objective reaction $nt$.
\end{itemize}
\paragraph{}
\paragraph{}This MCS algorithm can be divided into two phases as follows:
\paragraph{}

\noindent\colorbox{TeaGreen}{%
\begin{minipage}{\dimexpr\textwidth-1\fboxsep}
\paragraph{Preparatory phase}
\small{
\begin{enumerate}[(1)]
 \item Calculate the EFMs in the given networks.
 \item Define the objective reaction \texttt{obR}.
 \item Choose all EFMs where the reaction \texttt{obR} is non-zero and store it 
in the binary array \texttt{efms\_obR}.
 \item Initialise the arrays \texttt{mcss} and \texttt{precutsets} as follows:\;
Append $\{j\}$ to \texttt{mcss} if the reaction $j$ is essential, otherwise to 
\texttt{precutsets}.
\end{enumerate}
}
\paragraph{Main phase}
\small{
\begin{enumerate}[(5)]
 \item FOR i = 2 TO MAX\_CUTSETSIZE
  \begin{enumerate}[(5.1)]
   \item $new\_precutsets = \varnothing $;
   \item FOR j = 1 TO q
    \begin{enumerate}[(5.2.1)]
     \item Remove all sets from \texttt{precutsets} where the reaction
$j$ participates;
     \item Find all sets of reactions in \texttt{precutsets} that do not
cover any EFM in \texttt{efms\_obR} where reaction $j$ participates. Combine 
each
of these sets with reaction $j$ and store the new preliminary cut sets in
\texttt{temp\_precutsets};
     \item Drop all \texttt{temp\_precutsets} which are a superset of any of
the already determined minimal cut sets stored in \texttt{mcss};
     \item Find all retained \texttt{temp\_precutsets} which do now cover all
EFMs and append them to \texttt{mcss}. Append all others to
\texttt{new\_precutsets};
    \end{enumerate}
   \item IF \texttt{isEmpty(new\_precutsets)} BREAK; ELSE \texttt{precutsets} = 
\texttt{new\_precutsets};
  \end{enumerate}
 \begin{enumerate}[(6)]
  \item return \texttt{mcss};
 \end{enumerate}
\end{enumerate}
}
\end{minipage}
}

chapter2.tex

\begin{table}[htbp]
\caption[EFMs and MCSs of \textit{NetEx}, for the objective reaction 
\textit{PSynth}]{\textbf{EFMs and MCSs for the objective reaction 
\textit{PSynth}}.
The table shows the EFMs and MCSs of \textit{NetEx}, for the objective reaction 
\textit{PSynth}}
\begin{tabular}{lllllllll}
\toprule
 & \textbf{R1} & \textbf{R2} & \textbf{R3} & \textbf{R4} & \textbf{R5} & 
\textbf{R6} & \textbf{R7} & \textbf{\textit{Psynth}} \\ 
\midrule
\multicolumn{ 9}{l}{\textbf{Elementary Flux Modes}} \\ 
\midrule
EFM1 & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{0} 
& \multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{0} & 
\multicolumn{1}{r}{0} & \multicolumn{1}{r}{0} \\ 
EFM2 & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} 
& \multicolumn{1}{r}{0} & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} & 
\multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} \\ 
EFM3 & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} 
& \multicolumn{1}{r}{−1} & \multicolumn{1}{r}{−1} & \multicolumn{1}{r}{1} & 
\multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} \\ 
EFM4 & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} 
& \multicolumn{1}{r}{0} & \multicolumn{1}{r}{−1} & \multicolumn{1}{r}{0} & 
\multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} \\ 
EFM5 & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{1} 
& \multicolumn{1}{r}{−1} & \multicolumn{1}{r}{−2} & \multicolumn{1}{r}{0} & 
\multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} \\ 
EFM6 & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{2} & \multicolumn{1}{r}{1} 
& \multicolumn{1}{r}{1} & \multicolumn{1}{r}{0} & \multicolumn{1}{r}{0} & 
\multicolumn{1}{r}{1} & \multicolumn{1}{r}{1} \\
\midrule
\multicolumn{ 9}{l}{\textbf{Minimal Cut Sets}} \\
 \midrule
MCS0 &  &  &  &  &  &  &  & x \\ 
MCS1 &  &  & x &  &  &  &  &  \\ 
MCS2 & x &  &  &  &  & x &  &  \\ 
MCS3 &  &  &  &  &  & x & x &  \\ 
MCS4 &  & x &  & x &  &  &  &  \\ 
MCS5 &  & x &  &  & x &  &  &  \\ 
MCS6 & x &  &  & x & x &  &  &  \\ 
MCS7 &  &  &  & x & x & x &  &  \\ 
\bottomrule
\end{tabular}
\label{tab:klamt-netex-res-efms-mcss}
\end{table}

It often shows out the error:

! LaTeX Error: Option clash for package xcolor.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H   for immediate help.
 ...                                              

l.54 \usepackage
                {color}