Example problematic Latex file

%% bare_jrnl.tex
%% V1.4b
%% 2015/08/26
%% by Michael Shell
%% see http://www.michaelshell.org/
%% for current contact information.
%%
%% This is a skeleton file demonstrating the use of IEEEtran.cls
%% (requires IEEEtran.cls version 1.8b or later) with an IEEE
%% journal paper.
%%
%% Support sites:
%% http://www.michaelshell.org/tex/ieeetran/
%% http://www.ctan.org/pkg/ieeetran
%% and
%% http://www.ieee.org/

%%*************************************************************************
%% Legal Notice:
%% This code is offered as-is without any warranty either expressed or
%% implied; without even the implied warranty of MERCHANTABILITY or
%% FITNESS FOR A PARTICULAR PURPOSE!
%% User assumes all risk.
%% In no event shall the IEEE or any contributor to this code be liable for
%% any damages or losses, including, but not limited to, incidental,
%% consequential, or any other damages, resulting from the use or misuse
%% of any information contained here.
%%
%% All comments are the opinions of their respective authors and are not
%% necessarily endorsed by the IEEE.
%%
%% This work is distributed under the LaTeX Project Public License (LPPL)
%% ( http://www.latex-project.org/ ) version 1.3, and may be freely used,
%% distributed and modified. A copy of the LPPL, version 1.3, is included
%% in the base LaTeX documentation of all distributions of LaTeX released
%% 2003/12/01 or later.
%% Retain all contribution notices and credits.
%% ** Modified files should be clearly indicated as such, including  **
%% ** renaming them and changing author support contact information. **
%%*************************************************************************


% *** Authors should verify (and, if needed, correct) their LaTeX system  ***
% *** with the testflow diagnostic prior to trusting their LaTeX platform ***
% *** with production work. The IEEE's font choices and paper sizes can   ***
% *** trigger bugs that do not appear when using other class files.       ***                          ***
% The testflow support page is at:
% http://www.michaelshell.org/tex/testflow/



%\documentclass[journal,12pt,onecolumn,draftclsnofoot,]{IEEEtran}
\documentclass[journal]{IEEEtran}
%,12pt,onecolumn,draftclsnofootl
% If IEEEtran.cls has not been installed into the LaTeX system files,
% manually specify the path to it like:
% \documentclass[journal]{../sty/IEEEtran}

\usepackage{amsmath}
\interdisplaylinepenalty=2500



% Some very useful LaTeX packages include:
% (uncomment the ones you want to load)


% *** MISC UTILITY PACKAGES ***
%
%\usepackage{ifpdf}
% Heiko Oberdiek's ifpdf.sty is very useful if you need conditional
% compilation based on whether the output is pdf or dvi.
% usage:
% \ifpdf
%   % pdf code
% \else
%   % dvi code
% \fi
% The latest version of ifpdf.sty can be obtained from:
% http://www.ctan.org/pkg/ifpdf
% Also, note that IEEEtran.cls V1.7 and later provides a builtin
% \ifCLASSINFOpdf conditional that works the same way.
% When switching from latex to pdflatex and vice-versa, the compiler may
% have to be run twice to clear warning/error messages.






% *** CITATION PACKAGES ***
%
%\usepackage{cite}
% cite.sty was written by Donald Arseneau
% V1.6 and later of IEEEtran pre-defines the format of the cite.sty package
% \cite{} output to follow that of the IEEE. Loading the cite package will
% result in citation numbers being automatically sorted and properly
% "compressed/ranged". e.g., [1], [9], [2], [7], [5], [6] without using
% cite.sty will become [1], [2], [5]--[7], [9] using cite.sty. cite.sty's
% \cite will automatically add leading space, if needed. Use cite.sty's
% noadjust option (cite.sty V3.8 and later) if you want to turn this off
% such as if a citation ever needs to be enclosed in parenthesis.
% cite.sty is already installed on most LaTeX systems. Be sure and use
% version 5.0 (2009-03-20) and later if using hyperref.sty.
% The latest version can be obtained at:
% http://www.ctan.org/pkg/cite
% The documentation is contained in the cite.sty file itself.






% *** GRAPHICS RELATED PACKAGES ***
%
\ifCLASSINFOpdf
  % \usepackage[pdftex]{graphicx}
  % declare the path(s) where your graphic files are
  % \graphicspath{{../pdf/}{../jpeg/}}
  % and their extensions so you won't have to specify these with
  % every instance of \includegraphics
  % \DeclareGraphicsExtensions{.pdf,.jpeg,.png}
\else
  % or other class option (dvipsone, dvipdf, if not using dvips). graphicx
  % will default to the driver specified in the system graphics.cfg if no
  % driver is specified.
  % \usepackage[dvips]{graphicx}
  % declare the path(s) where your graphic files are
  % \graphicspath{{../eps/}}
  % and their extensions so you won't have to specify these with
  % every instance of \includegraphics
  % \DeclareGraphicsExtensions{.eps}
\fi
% graphicx was written by David Carlisle and Sebastian Rahtz. It is
% required if you want graphics, photos, etc. graphicx.sty is already
% installed on most LaTeX systems. The latest version and documentation
% can be obtained at:
% http://www.ctan.org/pkg/graphicx
% Another good source of documentation is "Using Imported Graphics in
% LaTeX2e" by Keith Reckdahl which can be found at:
% http://www.ctan.org/pkg/epslatex
%
% latex, and pdflatex in dvi mode, support graphics in encapsulated
% postscript (.eps) format. pdflatex in pdf mode supports graphics
% in .pdf, .jpeg, .png and .mps (metapost) formats. Users should ensure
% that all non-photo figures use a vector format (.eps, .pdf, .mps) and
% not a bitmapped formats (.jpeg, .png). The IEEE frowns on bitmapped formats
% which can result in "jaggedy"/blurry rendering of lines and letters as
% well as large increases in file sizes.
%
% You can find documentation about the pdfTeX application at:
% http://www.tug.org/applications/pdftex





% *** MATH PACKAGES ***
%
%\usepackage{amsmath}
% A popular package from the American Mathematical Society that provides
% many useful and powerful commands for dealing with mathematics.
%
% Note that the amsmath package sets \interdisplaylinepenalty to 10000
% thus preventing page breaks from occurring within multiline equations. Use:
%\interdisplaylinepenalty=2500
% after loading amsmath to restore such page breaks as IEEEtran.cls normally
% does. amsmath.sty is already installed on most LaTeX systems. The latest
% version and documentation can be obtained at:
% http://www.ctan.org/pkg/amsmath





% *** SPECIALIZED LIST PACKAGES ***
%
%\usepackage{algorithmic}
% algorithmic.sty was written by Peter Williams and Rogerio Brito.
% This package provides an algorithmic environment fo describing algorithms.
% You can use the algorithmic environment in-text or within a figure
% environment to provide for a floating algorithm. Do NOT use the algorithm
% floating environment provided by algorithm.sty (by the same authors) or
% algorithm2e.sty (by Christophe Fiorio) as the IEEE does not use dedicated
% algorithm float types and packages that provide these will not provide
% correct IEEE style captions. The latest version and documentation of
% algorithmic.sty can be obtained at:
% http://www.ctan.org/pkg/algorithms
% Also of interest may be the (relatively newer and more customizable)
% algorithmicx.sty package by Szasz Janos:
% http://www.ctan.org/pkg/algorithmicx




% *** ALIGNMENT PACKAGES ***
%
%\usepackage{array}
% Frank Mittelbach's and David Carlisle's array.sty patches and improves
% the standard LaTeX2e array and tabular environments to provide better
% appearance and additional user controls. As the default LaTeX2e table
% generation code is lacking to the point of almost being broken with
% respect to the quality of the end results, all users are strongly
% advised to use an enhanced (at the very least that provided by array.sty)
% set of table tools. array.sty is already installed on most systems. The
% latest version and documentation can be obtained at:
% http://www.ctan.org/pkg/array


% IEEEtran contains the IEEEeqnarray family of commands that can be used to
% generate multiline equations as well as matrices, tables, etc., of high
% quality.




% *** SUBFIGURE PACKAGES ***
%\ifCLASSOPTIONcompsoc
%  \usepackage[caption=false,font=normalsize,labelfont=sf,textfont=sf]{subfig}
%\else
%  \usepackage[caption=false,font=footnotesize]{subfig}
%\fi
% subfig.sty, written by Steven Douglas Cochran, is the modern replacement
% for subfigure.sty, the latter of which is no longer maintained and is
% incompatible with some LaTeX packages including fixltx2e. However,
% subfig.sty requires and automatically loads Axel Sommerfeldt's caption.sty
% which will override IEEEtran.cls' handling of captions and this will result
% in non-IEEE style figure/table captions. To prevent this problem, be sure
% and invoke subfig.sty's "caption=false" package option (available since
% subfig.sty version 1.3, 2005/06/28) as this is will preserve IEEEtran.cls
% handling of captions.
% Note that the Computer Society format requires a larger sans serif font
% than the serif footnote size font used in traditional IEEE formatting
% and thus the need to invoke different subfig.sty package options depending
% on whether compsoc mode has been enabled.
%
% The latest version and documentation of subfig.sty can be obtained at:
% http://www.ctan.org/pkg/subfig




% *** FLOAT PACKAGES ***
%
%\usepackage{fixltx2e}
% fixltx2e, the successor to the earlier fix2col.sty, was written by
% Frank Mittelbach and David Carlisle. This package corrects a few problems
% in the LaTeX2e kernel, the most notable of which is that in current
% LaTeX2e releases, the ordering of single and double column floats is not
% guaranteed to be preserved. Thus, an unpatched LaTeX2e can allow a
% single column figure to be placed prior to an earlier double column
% figure.
% Be aware that LaTeX2e kernels dated 2015 and later have fixltx2e.sty's
% corrections already built into the system in which case a warning will
% be issued if an attempt is made to load fixltx2e.sty as it is no longer
% needed.
% The latest version and documentation can be found at:
% http://www.ctan.org/pkg/fixltx2e


%\usepackage{stfloats}
% stfloats.sty was written by Sigitas Tolusis. This package gives LaTeX2e
% the ability to do double column floats at the bottom of the page as well
% as the top. (e.g., "\begin{figure*}[!b]" is not normally possible in
% LaTeX2e). It also provides a command:
%\fnbelowfloat
% to enable the placement of footnotes below bottom floats (the standard
% LaTeX2e kernel puts them above bottom floats). This is an invasive package
% which rewrites many portions of the LaTeX2e float routines. It may not work
% with other packages that modify the LaTeX2e float routines. The latest
% version and documentation can be obtained at:
% http://www.ctan.org/pkg/stfloats
% Do not use the stfloats baselinefloat ability as the IEEE does not allow
% \baselineskip to stretch. Authors submitting work to the IEEE should note
% that the IEEE rarely uses double column equations and that authors should try
% to avoid such use. Do not be tempted to use the cuted.sty or midfloat.sty
% packages (also by Sigitas Tolusis) as the IEEE does not format its papers in
% such ways.
% Do not attempt to use stfloats with fixltx2e as they are incompatible.
% Instead, use Morten Hogholm'a dblfloatfix which combines the features
% of both fixltx2e and stfloats:
%
% \usepackage{dblfloatfix}
% The latest version can be found at:
% http://www.ctan.org/pkg/dblfloatfix




%\ifCLASSOPTIONcaptionsoff
%  \usepackage[nomarkers]{endfloat}
% \let\MYoriglatexcaption\caption
% \renewcommand{\caption}[2][\relax]{\MYoriglatexcaption[#2]{#2}}
%\fi
% endfloat.sty was written by James Darrell McCauley, Jeff Goldberg and
% Axel Sommerfeldt. This package may be useful when used in conjunction with
% IEEEtran.cls'  captionsoff option. Some IEEE journals/societies require that
% submissions have lists of figures/tables at the end of the paper and that
% figures/tables without any captions are placed on a page by themselves at
% the end of the document. If needed, the draftcls IEEEtran class option or
% \CLASSINPUTbaselinestretch interface can be used to increase the line
% spacing as well. Be sure and use the nomarkers option of endfloat to
% prevent endfloat from "marking" where the figures would have been placed
% in the text. The two hack lines of code above are a slight modification of
% that suggested by in the endfloat docs (section 8.4.1) to ensure that
% the full captions always appear in the list of figures/tables - even if
% the user used the short optional argument of \caption[]{}.
% IEEE papers do not typically make use of \caption[]'s optional argument,
% so this should not be an issue. A similar trick can be used to disable
% captions of packages such as subfig.sty that lack options to turn off
% the subcaptions:
% For subfig.sty:
% \let\MYorigsubfloat\subfloat
% \renewcommand{\subfloat}[2][\relax]{\MYorigsubfloat[]{#2}}
% However, the above trick will not work if both optional arguments of
% the \subfloat command are used. Furthermore, there needs to be a
% description of each subfigure *somewhere* and endfloat does not add
% subfigure captions to its list of figures. Thus, the best approach is to
% avoid the use of subfigure captions (many IEEE journals avoid them anyway)
% and instead reference/explain all the subfigures within the main caption.
% The latest version of endfloat.sty and its documentation can obtained at:
% http://www.ctan.org/pkg/endfloat
%
% The IEEEtran \ifCLASSOPTIONcaptionsoff conditional can also be used
% later in the document, say, to conditionally put the References on a
% page by themselves.




% *** PDF, URL AND HYPERLINK PACKAGES ***
%
%\usepackage{url}
% url.sty was written by Donald Arseneau. It provides better support for
% handling and breaking URLs. url.sty is already installed on most LaTeX
% systems. The latest version and documentation can be obtained at:
% http://www.ctan.org/pkg/url
% Basically, \url{my_url_here}.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% New commands by me: - check at the end
%\usepackage{cite}
\usepackage{bm}
\newcommand{\matr}[1]{\bm{#1}}   % command to define matrices - change as desired
\newcommand{\vect}[1]{\bm{#1}}   % command to define vectors - change as desired
\usepackage{graphicx}
\usepackage{epstopdf}
\usepackage{lineno}
\linenumbers
%\usepackage{color}
%\usepackage{subfig}
\usepackage{hyperref}
\usepackage{cases}
\usepackage{amsfonts}
%\usepackage{nomencl}
%\makenomenclature
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


% *** Do not adjust lengths that control margins, column widths, etc. ***
% *** Do not use packages that alter fonts (such as pslatex).         ***
% There should be no need to do such things with IEEEtran.cls V1.6 and later.
% (Unless specifically asked to do so by the journal or conference you plan
% to submit to, of course. )


% correct bad hyphenation here
\hyphenation{op-tical net-works semi-conduc-tor}


\begin{document}
%
% paper title
% Titles are generally capitalized except for words such as a, an, and, as,
% at, but, by, for, in, nor, of, on, or, the, to and up, which are usually
% not capitalized unless they are the first or last word of the title.
% Linebreaks \\ can be used within to get better formatting as desired.
% Do not put math or special symbols in the title.
\title{An Innovative Marine Growth Detection System for Underwater Gliders}
%
%
% author names and IEEE memberships
% note positions of commas and nonbreaking spaces ( ~ ) LaTeX will not break
% a structure at a ~ so this keeps an author's name from being broken across
% two lines.
% use \thanks{} to gain access to the first footnote area
% a separate \thanks must be used for each paragraph as LaTeX2e's \thanks
% was not built to handle multiple paragraphs
%

\author{Author~1,
        Author~2,
        and~Author~3% <-this % stops a space
\thanks{The research leading to these results has received funding from

Author 1 is with}% <-this % stops a space
\thanks{Author 2 is with}% <-this % stops a space
\thanks{Manuscript received July, 2020; revised YY, 2020.}}

% note the % following the last \IEEEmembership and also \thanks -
% these prevent an unwanted space from occurring between the last author name
% and the end of the author line. i.e., if you had this:
%
% \author{....lastname \thanks{...} \thanks{...} }
%                     ^------------^------------^----Do not want these spaces!
%
% a space would be appended to the last name and could cause every name on that
% line to be shifted left slightly. This is one of those "LaTeX things". For
% instance, "\textbf{A} \textbf{B}" will typeset as "A B" not "AB". To get
% "AB" then you have to do: "\textbf{A}\textbf{B}"
% \thanks is no different in this regard, so shield the last } of each \thanks
% that ends a line with a % and do not let a space in before the next \thanks.
% Spaces after \IEEEmembership other than the last one are OK (and needed) as
% you are supposed to have spaces between the names. For what it is worth,
% this is a minor point as most people would not even notice if the said evil
% space somehow managed to creep in.



% The paper headers
\markboth{Journal of Oceanic Engineering,~Vol.~XX, No.~Y, July~2020}%
{A Novel Title}
% The only time the second header will appear is for the odd numbered pages
% after the title page when using the twoside option.
%
% *** Note that you probably will NOT want to include the author's ***
% *** name in the headers of peer review papers.                   ***
% You can use \ifCLASSOPTIONpeerreview for conditional compilation here if
% you desire.




% If you want to put a publisher's ID mark on the page you can do it like
% this:
%\IEEEpubid{0000--0000/00\$00.00~\copyright~2015 IEEE}
% Remember, if you use this you must call \IEEEpubidadjcol in the second
% column for its text to clear the IEEEpubid mark.



% use for special paper notices
%\IEEEspecialpapernotice{(Invited Paper)}




% make the title area
\maketitle

% As a general rule, do not put math, special symbols or citations
% in the abstract or keywords.
\begin{abstract}
Marine
\end{abstract}

% Note that keywords are not normally used for peerreview papers.
\begin{IEEEkeywords}
Word 1, word 2, word 3.
\end{IEEEkeywords}


% For peer review papers, you can put extra information on the cover
% page as needed:
% \ifCLASSOPTIONpeerreview
% \begin{center} \bfseries EDICS Category: 3-BBND \end{center}
% \fi
%
% For peerreview papers, this IEEEtran command inserts a page break and
% creates the second title. It will be ignored for other modes.
\IEEEpeerreviewmaketitle



\section{Introduction}
% The very first letter is a 2 line initial drop letter followed
% by the rest of the first word in caps.
%
% form to use if the first word consists of a single letter:
% \IEEEPARstart{A}{demo} file is ....
%
% form to use if you need the single drop letter followed by
% normal text (unknown if ever used by the IEEE):
% \IEEEPARstart{A}{}demo file is ....
%
% Some journals put the first two words in caps:
% \IEEEPARstart{T}{his demo} file is ....
%
% Here we have the typical use of a "T" for an initial drop letter
% and "HIS" in caps to complete the first word.
Underwater


% Can use something like this to put references on a page
% by themselves when using endfloat and the captionsoff option.
\ifCLASSOPTIONcaptionsoff
  \newpage
\fi



% trigger a \newpage just before the given reference
% number - used to balance the columns on the last page
% adjust value as needed - may need to be readjusted if
% the document is modified later
%\IEEEtriggeratref{8}
% The "triggered" command can be changed if desired:
%\IEEEtriggercmd{\enlargethispage{-5in}}

% references section

% can use a bibliography generated by BibTeX as a .bbl file
% BibTeX documentation can be easily obtained at:
% http://mirror.ctan.org/biblio/bibtex/contrib/doc/
% The IEEEtran BibTeX style support page is at:
% http://www.michaelshell.org/tex/ieeetran/bibtex/
\bibliographystyle{IEEEtran}
% argument is your BibTeX string definitions and bibliography database(s)
%\bibliography{IEEEabrv,../bib/paper}
%
% <OR> manually copy in the resultant .bbl file
% set second argument of \begin to the number of references
% (used to reserve space for the reference number labels box)
\bibliography{../library}

% biography section
%
% If you have an EPS/PDF photo (graphicx package needed) extra braces are
% needed around the contents of the optional argument to biography to prevent
% the LaTeX parser from getting confused when it sees the complicated
% \includegraphics command within an optional argument. (You could create
% your own custom macro containing the \includegraphics command to make things
% simpler here.)
%\begin{IEEEbiography}[{\includegraphics[width=1in,height=1.25in,clip,keepaspectratio]{mshell}}]{Michael Shell}
% or if you just want to reserve a space for a photo:

%\begin{IEEEbiography}{Michael Shell}
%Biography text here.
%\end{IEEEbiography}

% if you will not have a photo at all:
%\begin{IEEEbiographynophoto}{John Doe}
%Biography text here.
%\end{IEEEbiographynophoto}

% insert where needed to balance the two columns on the last page with
% biographies
%\newpage

%\begin{IEEEbiographynophoto}{Jane Doe}
%Biography text here.
%\end{IEEEbiographynophoto}

% You can push biographies down or up by placing
% a \vfill before or after them. The appropriate
% use of \vfill depends on what kind of text is
% on the last page and whether or not the columns
% are being equalized.

%\vfill

% Can be used to pull up biographies so that the bottom of the last one
% is flush with the other column.
%\enlargethispage{-5in}



% that's all folks
\end{document}