Problems: Appendices, ToC, and Bookmarks

[MRK]

Dear all,
I am writing my dissertation. I am have problems with producing the
desirable pdf. The problems I am getting are:
1. No bookmark for Title Page or ToC.
2. List of Figures and List of Tables bookmarks point to Title Page.
3. Bibliography and vita are bookmarked under Part III (Appendices).
4. ToC lists a page number for each of the Parts’ pages.

My main file is copied below. What I want to end up with is:
1. Top level bookmarks with correct targets for:
a. Title Page
b. ToC
c. List of Figures
d. List of Tables
e. Main matter components
f. Bibliography
g. Vita
h. Appendices
2. I want each of the Parts’ page not to have a page number on the
ToC.

I tried using the appendices environment but kept receiving an error
message about redefining a command that was not defined before. My
guess is that the Appendix package is running into a conflict with
another package. My problem is that I cannot figure out which one is
the offensive package.

Any help is greatly appreciated.

Best regards,
MRK
=============
%
% This is file `iuthesis.tex',
% generated with the docstrip utility.
%
% The original source files were:
%
% iuthesis.dtx (with options: `docs')
% IUThesis Document Class (N. Danner)
%
% iuthesis: Document class for IU Thesis.
% N. Danner (nda...@indiana.edu)
% Copyright 1999
%
% RCS Info:
% iuthesis.dtx,v 1.2.0.23 1999/06/04 14:30:00 ndanger Exp
%
\def\fileversion{1.2.0.23}
\def\filedate{1999/06/04}
\errorcontextlines=999
%\raggedbottom
%\documentclass[letterpaper,14pt,fleqn]{report}
\documentclass[12pt,reqno,final]{iuthesis}
\renewcommand{\thepart}{\Roman{part}}
\usepackage{listings} % identify the language with
\lstset{language=FORTRAN}
\usepackage{verbatim}
\usepackage{fancyvrb}
\usepackage{rotating}
\usepackage[usenames]{color} % to include .jpg figures
\usepackage{graphicx} % to include .jpg figures
\usepackage{natbib}
\usepackage[version=3]{mhchem}
\usepackage{setspace}
\usepackage{caption}
\usepackage{lscape}
\DeclareCaptionFont{singlespacing}{\singlespacing}
%The following six lines make it possible for Figure number to go
continuous over all chapters using the package: {remreset}.
\usepackage{remreset}
\makeatletter
\@removefromreset{figure}{chapter}
\makeatother
\renewcommand{\thefigure}{\arabic{figure}}
\makeatother
\usepackage{morehelp}
\usepackage[centertags]{amsmath}
\usepackage[title,titletoc,header]{appendix}
\usepackage{datetime}
\usepackage{fancyhdr}
\usepackage{ifpdf}
%\ifpdf
\usepackage[
pdftex,
pagebackref = true,
breaklinks = true,
colorlinks = true,
linkcolor = red,
anchorcolor = red,
citecolor = blue,
filecolor = red,
urlcolor = red,
pdfborder={0 0 0}
bookmarks,
%bookmarksopen,
pdffitwindow,
pdftitle = {My Dissertation},
pdfauthor = {Me},
]{hyperref}
\title{Geol. of the IL Basin}
\author{}
\advisor{} \secondreader{}
\thirdreader{}
\fourthreader{} \fifthreader{}

\department{Geological Sciences}
\submitdate{2 May 2011}
\copyrightyear{~\copyright ~2011}

\begin{document}
%
%
\lstset{language=Fortran}
% Dedication
% \begin{dedication}
% \textbf{Dedication}\\
% \bigskip
% \par
% To my parents, wife, and daughters\\
% \par
% \ldots \par \ldots \par \ldots
% \end{dedication}

% Dedication
\begin{dedication}
To my parents, wife\\
\par
\ldots \par \ldots \par \ldots
\end{dedication}

% Acknowledgements
\begin{acknowledgements}
Thank God, advisor, committee members, IUB computing facilities, and
Aramco\\
\par
\ldots \par \ldots \par \ldots
\end{acknowledgements}

% Abstract
\begin{abstract}
In this dissertation, I will discuss\\
\par
\ldots \par \ldots \par \ldots
\end{abstract}

\frontmatter


% generate the Title
\maketitle
% generate the Signature page
\signaturepage
% generate the Copyright page
\copyrightpage
% generate the Dedication page
\makededication[2in]
% generate the Acknowledgement page
\makeack
% generate the Abstract page
\makeabstract
% insert the table of contents
\tableofcontents
%{\texorpdfstring{\tableofcontents}{Table of Contents}}
% insert the list of figures
\listoffigures
% insert the list of tables
\listoftables

\mainmatter
\part{Reaction-Transport}
\include{chapter_01}
\include{chapter_02}
%\include{chapter_03}
%\include{chapter_04}
%
%
\part{Stratigraphic Modeling}
\include{chapter_05}
%

\backmatter
\include{vita}
%
%
\part{Appendices}
\appendix
%\appendixpage
%\addappheadtotoc
%\appendixname
%\noappendicestocpagenum
%
%\begin{appendices}
\include{MeshGen_Code}
\include{Rxn_Rate}
\include{Chem_Transport}
%\end{appendices}
%
%
\part{Documentation}
{\setlength{\baselineskip}{0.75\baselineskip}
\bibliographystyle{agufull}
%\bibliography{mrk-thesis}\par}
\bibliography{mrk-thesis-full}\par}
\backmatter
\include{vita}
%

\end{document}
%
% End of file `iuthesis.tex'.

[Peter Flynn]

On Fri, Apr 8, 2011 at 11:10 PM, MRK <mrkq...@gmail.com> wrote:

Dear all,
I am writing my dissertation.  I am have problems with producing the
desirable pdf.  

After downloading iuthesis.cls, morehelp.sty, and morehelp.eng I managed to get this to compile with only one error (linebreak failer because you have not provided an author name). If you attach an example, please make sure it works (or fails!) properly :-)

Have you read the documentation? That is, have you processed iuthesis.dtx with LaTeX and created some output describing how to use the package?

The problems I am getting are:
1. No bookmark for Title Page or ToC.

It is normal for the Title Page not to be bookmarked because it is the first page. It doesn't need one.
 

2. List of Figures and List of Tables bookmarks point to Title Page.

I'm afraid I don't understand what IUthesis does for the ToC, LoF, and LoT. The code appears to be broken (it produces the list, but puts the heading afterwards, which is an error). You must ask them to fix this.
 

3. Bibliography and vita are bookmarked under Part III (Appendices).

Possibly the same problem.
 

4. ToC lists a page number for each of the Parts’ pages.

I think you need to start writing some text. It's possible that when there is real text in the document, some of these problems may disappear. The documentation is rather vague about why they have changed the ToC, LoF, and LoT.

According to iuthesis.dtx, this package was written in 1999 when pdflatex and hyperref were in their infancy, so it is not reasonable to expect this package to work with hyperlinks to the same extent as a modern package. You should contact the author if possible, or the Bloomington Graduate School at Indiana University. 

 

My main file is copied below.  

You should not call your thesis filename iuthesis.tex. Call it something meaningful like qatif-thesis.tex and keep the filenames iuthesis.* for the components of the iuthesis package, so that they don't get mixed up.

What I want to end up with is:
1. Top level bookmarks  with correct targets for:
a. Title Page
b. ToC
c. List of Figures
d. List of Tables
e. Main matter components
f. Bibliography
g. Vita
h. Appendices
2. I want each of the Parts’ page not to have a page number on the
ToC.

I tried using the appendices environment but kept receiving an error
message about redefining a command that was not defined before.  My
guess is that the Appendix package is running into a conflict with
another package.  My problem is that I cannot figure out which one is
the offensive package.

Nor can I. You need to contact them about this.

///Peter
 

[MRK]

Thank you very much Peter for the detailed response. I did run LaTeX
on the original files. I guess your thought this document class being
an old one may be causing the problems is quite plausible. I looked
around the IUB grad. school site for newer version, but there was
none. I will work around the problems.

Many thanks again.

Mohammad



On Apr 10, 5:00 pm, Peter Flynn <anglebrac...@gmail.com> wrote:

> On Fri, Apr 8, 2011 at 11:10 PM, MRK <mrkqa...@gmail.com> wrote:
> > Dear all,
> > I am writing my dissertation.  I am have problems with producing the
> > desirable pdf.
>
> After downloading iuthesis.cls, morehelp.sty, and morehelp.eng I managed to
> get this to compile with only one error (linebreak failer because you have
> not provided an author name). If you attach an example, please make sure it
> works (or fails!) properly :-)
>
> Have you read the documentation? That is, have you processed iuthesis.dtx
> with LaTeX and created some output describing how to use the package?
>
> The problems I am getting are:
>
> > 1. No bookmark for Title Page or ToC.
>
> It is normal for the Title Page not to be bookmarked because it is the first
> page. It doesn't need one.
>
> > 2. List of Figures and List of Tables bookmarks point to Title Page.
>
> I'm afraid I don't understand what IUthesis does for the ToC, LoF, and LoT.

> The code appears to be broken (it produces the list, but puts the heading *
> afterwards*, which is an error). You must ask them to fix this.

>
> > 3. Bibliography and vita are bookmarked under Part III (Appendices).
>
> Possibly the same problem.
>
> > 4. ToC lists a page number for each of the Parts’ pages.
>
> I think you need to start writing some text. It's possible that when there
> is real text in the document, some of these problems may disappear. The
> documentation is rather vague about why they have changed the ToC, LoF, and
> LoT.
>
> According to iuthesis.dtx, this package was written in 1999 when pdflatex
> and hyperref were in their infancy, so it is not reasonable to expect this
> package to work with hyperlinks to the same extent as a modern package. You
> should contact the author if possible, or the Bloomington Graduate School at
> Indiana University.
>
> > My main file is copied below.
>

> You should not call *your* thesis filename iuthesis.tex. Call it something