Here is the github link uathesis where I am using to write up my dissertation with the newer class uathesis.
All I am doing is to replace my text body with that of the templates.
Here is the dissertation.tex file:
\documentclass[dissertation,CC-BY-ND]{uathesis}
% Package Usage
\usepackage[ruled,boxed,noend]{algorithm2e}
\usepackage{graphicx}
\usepackage{natbib} % natbib is available on most systems, and is
% terribly handy.
% If you want to use a different Bibliography package,
% you should be able to, just change this
% and the \bibliographystyle command below. Be warned
% that you may need to do a little hacking to get
% the REFERENCES item to show up in your TOC.
\usepackage{aastex_hack} % Allows other AASTEX functionality.
\usepackage[bookmarks,colorlinks=true,urlcolor=black,linkcolor=black,citecolor=black]{hyperref}
% Set up some values.
\completetitle{My Lovely Dissertation}
\fullname{Bob Bob Loblaw} % Grad college wants your full name here.
\degreename{Doctor of Philosophy} % Title of your degree.
\begin{document}
% Set up the title page
\maketitlepage
{DEPARTMENT OF COMPUTER SCIENCE} % Title of your department.
{2013}
\approval
{1 January 1922} % Defense Date
{Arnold Abrams} % Dissertation Director
{Billy Boy} % 1st committee member
{Carl Crow} % 2nd committee member
{Donna Dood} % 3rd committee member
{Edgar Elm} % 4th committee member (leave empty if None)
{} % 5th committee member (leave empty if None)
% Include the ``Statement by Author'' for Dissertations
\statementbyauthor
% Include the ``Acknowledgements''
\incacknowledgements{acknowledgements}
\incdedication{dedication}
\tableofcontents
\listoffigures
\listoftables
\incabstract{abstract}
\include{mainmatter/introduction}
\appendix
\include{appendix_A}
\renewcommand{\baselinestretch}{1} % changing the value
\small\normalsize % switch size to make the value take
\bibliographystyle{uabibnat}
\bibliography{bibliography}
\end{document}
Here is the introduction.tex file inside mainmatter folder:
\chapter{INTRODUCTION\label{chapter:introduction}}
Some Statement \citep[hereafter ETHOS paper]{2016MNRAS.460.1399V}. Some other statement \citep{2016MNRAS.463.1666C}. Still another statement \citep{1993MNRAS.264..201K,1999ApJ...522...82K,1999ApJ...524L..19M}. Yet another statement \citep{2017arXiv171106267K}. The final statement \citep{Tolman511,1934rtc..book.....T,1935ApJ....82..302H,1996ApJ...456L..79P}.
First statement \citep{2004MNRAS.348..421N}, and \citep{2000ApJ...543..552S,2004MNRAS.348..421N,2005ARA&A..43..861W}. Second statement \citep{2017arXiv170401634R}. Third statement \citep{2011ApJ...743...82M} and \citep{2014ApJ...782L..29R}, as well as \citep{2005ARA&A..43..861W,2015ApJ...800....7N}. Forth statement \citep{2005pgqa.conf..231L}. Final statement \citep{2011MNRAS.418.1796F,2011MNRAS.412L.118F,2011MNRAS.413L..51K,2012MNRAS.421.2809V,2012MNRAS.424.2292G,2013ApJ...775...78F,2013ApJ...765...89S,2014ApJ...780...74F,2015MNRAS.449..987F}.
First Statement \citep{2012arXiv1209.3272T}. Second statement \citep{1986ApJS...61..249W,1989ApJ...344..567T,1991ApJS...77....1L,2000ApJ...543..552S,2003MNRAS.346.1103P,2004PASP..116..622P,2008MNRAS.388.1349E,2009ApJ...696.1543P,2009A&A...505.1087N,2012A&A...547L...1N,2013yCat..35560141Z,2013A&A...556A.140Z,2015MNRAS.452..217C,2016MNRAS.456.4488S}. Third statement \citep{2012A&A...547L...1N} while \citep{2017arXiv170401634R} and \citep{2018MNRAS.473L..54K}.
First statement \citep{2006ApJ...652..994C,2011MNRAS.417..304L,2008ApJ...687..745C} and stars \citep{2011MNRAS.417..304L,2008ApJ...687..745C,2018ApJ...856L..12N,2011MNRAS.410.2237P,2010MNRAS.402.2520S,2005ApJ...623..767J,2003AAS...20314504C,2001APS..APRB14007G,2000ASPC..215..287C,1998ApJ...501L..11M}.
First statement \citep{1999MNRAS.305L..21B,2001ApJ...554...85W,2003A&A...409..835F,2004MNRAS.347..813H,2005ApJ...635...60T}.
First statement \citep{2017arXiv170401634R}. \cite{2017hsa9.conf..193P} have shown this. Second statement \cite{2018MNRAS.480.4702P}.
My bibliography.bib file of the project is a lengthy one and as soon as it is replaced with the empty one in the project, I am receiving a bunch of error messages as follows all related to the entries of the bibliography file:
Package natbib Error: Bibliography not compatible with author-year citations.
(natbib) Press <return> to continue in numerical citation style.
See the natbib package documentation for explanation.
Type H <return> for immediate help.
...
l.87 ...mand\NAT@force@numbers{}\NAT@force@numbers
Check the bibliography entries for non-compliant syntax,
or select author-year BibTeX style, e.g. plainnat
output.bbl, line 220
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.231 \newblock \doi
{10.1086/311448}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 234
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.234 ...ucher-Gigu{\`e}re}}]{2011ApJ...743...82M}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 239
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.239 \newblock \doi
{10.1088/0004-637X/743/1/82}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 242
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.242 ...adel}, and {Tozzi}}]{1999ApJ...524L..19M}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 247
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.247 \newblock \doi
{10.1086/312287}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 250
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.250 {Hernquist}}]{2004MNRAS.348..421N}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 255
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.255 \newblock \doi
{10.1111/j.1365-2966.2004.07393.x}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 259
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.259 {Zwaan}}]{2018ApJ...856L..12N}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 263
Missing $ inserted.
Check that your $'s match around math expressions. If they do, then you've probably used a symbol in normal text that needs to be in math mode. Symbols such as subscripts ( _ ), integrals ( \int ), Greek letters ( \alpha, \beta, \delta ), and modifiers (\vec{x}, \tilde{x} ) must be written in math mode. See the full list here.If you intended to use mathematics mode, then use $ … $ for 'inline math mode', $$ … $$ for 'display math mode' or alternatively \begin{math} … \end{math}.
Learn more
<inserted text>
$
l.263 ...from a Galaxy Associated with a z {\tilde
} 2.2
I've inserted a begin-math/end-math symbol since I think
you left one out. Proceed, with fingers crossed.
! Missing { inserted.
<to be read again>
}
l.263 ...rom a Galaxy Associated with a z {\tilde}
2.2
A left brace was mandatory here, so I've put one in.
You might want to delete and/or insert some corrections
so that I will find a matching right brace soon.
(If you're confused by all this, try typing `I}' now.)
output.bbl, line 264
Missing } inserted.
<inserted text>
}
l.264 Damped Ly{$
\alpha$} Absorber}.
I've inserted something that you may have forgotten.
(See the <inserted text> above.)
With luck, this will get me unwedged. But if you
really didn't forget anything, try typing `2' now; then
my insertion and my current dilemma will both disappear.
! Missing $ inserted.
<inserted text>
$
l.264 Damped Ly{$\alpha
$} Absorber}.
I've inserted a begin-math/end-math symbol since I think
you left one out. Proceed, with fingers crossed.
output.bbl, line 266
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.266 \newblock \doi
{10.3847/2041-8213/aab5b1}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 269
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.269 {Wolfe}}]{2015ApJ...800....7N}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 273
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.273 \newblock \doi
{10.1088/0004-637X/800/1/7}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
[14]
output.bbl, line 279
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.279 {York}}]{2012A&A...547L...1N}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 289
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.289 \newblock \doi
{10.1051/0004-6361/201220259}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 292
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.292 {Srianand}}]{2009A&A...505.1087N}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 297
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.297 \newblock \doi
{10.1051/0004-6361/200912768}.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 300
LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.300 Carvalho}}]{1996ApJ...456L..79P}
Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
output.bbl, line 305
.
.
.
.
! Undefined control sequence.
l.81 \bibcite
{2016MNRAS.460.1399V}{{55}{2016}{{{Vogelsberger} et~al.}}{{{Vog...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.aux, line 82
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.82 \bibcite
{2001ApJ...554...85W}{{56}{2001}{{{Wechsler} et~al.}}{{{Wechsle...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
! Undefined control sequence.
l.83 \bibcite
{2005ARA&A..43..861W}{{57}{2005}{{{Wolfe} et~al.}}{{{Wolfe}, {G...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.aux, line 83
Misplaced alignment tab character &.
You have placed an alignment tab character '&' in the wrong place. If you want to align something, you must write it inside an align environment such as \begin{align} … \end{align}, \begin{tabular} … \end{tabular}, etc. If you want to write an ampersand '&' in text, you must write \& instead.
Learn more
l.83 \bibcite{2005ARA&
A..43..861W}{{57}{2005}{{{Wolfe} et~al.}}{{{Wolfe}, {G...
I can't figure out why you would want to use a tab mark
here. If you just want an ampersand, the remedy is
simple: Just type `I\&' now. But if some right brace
up above has ended a previous alignment prematurely,
you're probably due for more error messages, and you
might try typing `S' now just to see what is salvageable.
! Undefined control sequence.
l.84 \bibcite
{1986ApJS...61..249W}{{58}{1986}{{{Wolfe} et~al.}}{{{Wolfe}, {T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.aux, line 85
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.85 \bibcite
{2013yCat..35560141Z}{{59}{2013{}}{{{Zafar} et~al.}}{{{Zafar}, ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
! Undefined control sequence.
l.86 \bibcite
{2013A&A...556A.140Z}{{60}{2013{}}{{{Zafar} et~al.}}{{{Zafar}, ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.aux, line 86
Misplaced alignment tab character &.
You have placed an alignment tab character '&' in the wrong place. If you want to align something, you must write it inside an align environment such as \begin{align} … \end{align}, \begin{tabular} … \end{tabular}, etc. If you want to write an ampersand '&' in text, you must write \& instead.
Learn more
l.86 \bibcite{2013A&
A...556A.140Z}{{60}{2013{}}{{{Zafar} et~al.}}{{{Zafar}, ...
I can't figure out why you would want to use a tab mark
here. If you just want an ampersand, the remedy is
simple: Just type `I\&' now. But if some right brace
up above has ended a previous alignment prematurely,
you're probably due for more error messages, and you
might try typing `S' now just to see what is salvageable.
)
! Undefined control sequence.
\@dofilelist ->\Call@AtVeryEndDocument
\Call@AtEndAfterFileList
l.133 \end{document}
output.aux, line 133
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
\@dofilelist ...Document \Call@AtEndAfterFileList
l.133 \end{document}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
output.bbl, line 401
Command \~ invalid in math mode on input line 401.
I am not sure what is causing the error but it seems that all of them are related to the bibliography file which I don't know if something is wrong with it.
Persistent Error Message:
Undefined control sequence.
The compiler is having trouble understanding a command you have used. Check that the command is spelled correctly. If the command is part of a package, make sure you have included the package in your preamble using \usepackage{...}.
Learn more
l.45 \newblock \jcap
{\bf 11}, 059 (2012).
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
[83
Best Answer
Bases on your given link in the question and the bib file you gave in your last question I was able to create a MWE for your case here. See the code later.
The error message you got
Indicates, that you have missed to add options
numberstonatbibto get a numbered bibliography ([1]) and not a bibliography following author-year citations ([CMQ2016]).To get a simple MWE I just deleted the
\included files and simply copied a small code for indroduction (you gave in the last question, it fit's better to your given bib file) into that MWE. So I got the resulting MWEwhich results in the following bibliography without errors: