Embedding Only TrueType Fonts Using XeLaTeX

Question

Background: I'm writing my thesis and per the department guidelines, I have to use TrueType fonts and they need to be embedded in the PDF.

Now, I have managed to change everything into Computer Modern Unicode (CMU) or Latin Modern for monospace font, but the output file says there are other font types (Type 1) embedded in the PDF (and there are so many duplicates for some reason):

My question is, how can I make sure only TrueType fonts are being used? I searched for these fonts in the preamble:

\usepackage[paper= letterpaper,left=1.5in,right=1in,top=1.25in,bottom=1.25in]{geometry}
\usepackage{verbatim}
\usepackage{latexsym}
\usepackage{mathchars}
\usepackage{setspace}

\usepackage[english]{babel}
\usepackage{blindtext}
\usepackage[compact]{titlesec} % removing extra white space with "titlespacing"
\usepackage[labelsep=period]{caption} % adds dots instead of colon
\usepackage[none]{hyphenat} % removes word hyphenating
\usepackage[document]{ragged2e}% no word-wrap justification
\setlength{\RaggedRightParindent}{\parindent}
\usepackage{etoolbox} % to fix the problem caused by above code -- see "AtBeginEnvironment"
\usepackage{txfonts}  % for upright greek letters | use $\betaup$ or $\muup$
\usepackage{bibentry} % for full citation inline
\usepackage{textcomp} % for copyright and other symbols
\usepackage{datetime} % for date
\usepackage{tabto} % for tabbing (see committee.tex)
\usepackage{fontspec} % to import fonts via XeTeX
\setmainfont{CMU Serif} % TrueType font of Computer Modern
\setmonofont{Latin Modern Mono Prop} % Mono TrueType font
\setromanfont{CMU Serif} % TrueType
\setsansfont{CMU Serif} % TrueType
\usepackage{enumitem} % for better item listing and change its spacing
\usepackage{fixltx2e} % for textsubscript{}
\usepackage[natbibapa]{apacite} % for bibliography % use apacite or apalike
\usepackage[nottoc,notlof,notlot]{tocbibind} % to fix bib href jump
\usepackage{hyperref} % for bibliography
\usepackage{setspace} % Allows for \singlespacing and \doublespacing command
\usepackage[super]{nth} % for creating 1st, 2nd, etc. using \nth{1}, \nth{2}
\usepackage{tabu} % for more adjustments for table
\usepackage{tabularx} % for table
\usepackage{placeins} % for table -- add \FloatBarrier before and after begin/end table
\usepackage[flushleft]{threeparttable} % for table
\usepackage{booktabs,caption,fixltx2e} % caption width setup (captionsetup) is further down
\usepackage[space]{grffile} % for spacing in graphics path name
\usepackage{graphicx} % for images - related: use [float] package for placement
\graphicspath{ {/Users/Payam/Google Drive/Thesis/images/} } % image directory
\usepackage{gensymb} % for degree sign \degree
\usepackage[table,xcdraw]{xcolor} % for table

\usepackage{xpatch} % for two spaces after period
\makeatletter % for two spaces after period
\xpatchcmd{\selectfont} % for two spaces after period
  {\pickup@font\font@name} % for two spaces after period
  {\pickup@font\font@name\fontdimen7\font=\fontdimen2\font}
 {}{}
\makeatother % for two spaces after period
\usepackage{tocloft} % changing TOC boldness

\usepackage{color} % for color text
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \let\oldtextbf\textbf % changes all bolod text color to red
 \renewcommand{\textbf}[1]{\textcolor{red}{\oldtextbf{#1}}} % changes bold text color to red
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Remove the two lines above after userpackage{color} before submitting  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


% Removing extra space
\titlespacing{\section}{0pt}{*0}{*0}
\titlespacing{\subsection}{0pt}{*0}{*0}
\titlespacing{\subsubsection}{0pt}{*0}{*0}

%%% This is for shortauthor references
\defcitealias{CDC2012}{CDC, 2012}
\defcitealias{CDCfasd}{CDC, 2014}
\defcitealias{NIHalcohol}{NIH, 2015}
\defcitealias{NIHcpt1}{NIH, 2014}
\defcitealias{DoHaHS2014}{HSS, 2014}

% Removes bolded TOC entries
\renewcommand\cftchapfont{\mdseries}
\renewcommand\cftchappagefont{\mdseries}

% centers table tex vertically when use "m"
\renewcommand\tabularxcolumn[1]{>{\Centering}m{#1}}

\input{blocked.sty}
\input{uhead.sty}
\input{boxit.sty}
\input{icthesis.sty}

\newcommand{\ipc}{{\sf ipc}}

\newcommand{\Prob}{\bbbp}
\newcommand{\Real}{\bbbr}
\newcommand{\real}{\Real}
\newcommand{\Int}{\bbbz}
\newcommand{\Nat}{\bbbn}

\newcommand{\NN}{{\sf I\kern-0.14emN}}   % Natural numbers
\newcommand{\ZZ}{{\sf Z\kern-0.45emZ}}   % Integers
\newcommand{\QQQ}{{\sf C\kern-0.48emQ}}   % Rational numbers
\newcommand{\RR}{{\sf I\kern-0.14emR}}   % Real numbers
\newcommand{\KK}{{\cal K}}
\newcommand{\OO}{{\cal O}}
\newcommand{\AAA}{{\bf A}}
\newcommand{\HH}{{\bf H}}
\newcommand{\II}{{\bf I}}
\newcommand{\LL}{{\bf L}}
\newcommand{\PP}{{\bf P}}
\newcommand{\PPprime}{{\bf P'}}
\newcommand{\QQ}{{\bf Q}}
\newcommand{\UU}{{\bf U}}
\newcommand{\UUprime}{{\bf U'}}
\newcommand{\zzero}{{\bf 0}}
\newcommand{\ppi}{\mbox{\boldmath $\pi$}}
\newcommand{\aalph}{\mbox{\boldmath $\alpha$}}
\newcommand{\bb}{{\bf b}}
\newcommand{\ee}{{\bf e}}
\newcommand{\mmu}{\mbox{\boldmath $\mu$}}
\newcommand{\vv}{{\bf v}}
\newcommand{\xx}{{\bf x}}
\newcommand{\yy}{{\bf y}}
\newcommand{\zz}{{\bf z}}
\newcommand{\oomeg}{\mbox{\boldmath $\omega$}}
\newcommand{\res}{{\bf res}}
\newcommand{\cchi}{{\mbox{\raisebox{.4ex}{$\chi$}}}}
%\newcommand{\cchi}{{\cal X}}
%\newcommand{\cchi}{\mbox{\Large $\chi$}}

% Logical operators and symbols
\newcommand{\imply}{\Rightarrow}
\newcommand{\bimply}{\Leftrightarrow}
\newcommand{\union}{\cup}
\newcommand{\intersect}{\cap}
\newcommand{\boolor}{\vee}
\newcommand{\booland}{\wedge}
\newcommand{\boolimply}{\imply}
\newcommand{\boolbimply}{\bimply}
\newcommand{\boolnot}{\neg}
\newcommand{\boolsat}{\!\models}
\newcommand{\boolnsat}{\!\not\models}


\newcommand{\op}[1]{\mathrm{#1}}
\newcommand{\s}[1]{\ensuremath{\mathcal #1}}

% Properly styled differentiation and integration operators
\newcommand{\diff}[1]{\mathrm{\frac{d}{d\mathit{#1}}}}
\newcommand{\diffII}[1]{\mathrm{\frac{d^2}{d\mathit{#1}^2}}}
\newcommand{\intg}[4]{\int_{#3}^{#4} #1 \, \mathrm{d}#2}
\newcommand{\intgd}[4]{\int\!\!\!\!\int_{#4} #1 \, \mathrm{d}#2 \, \mathrm{d}#3}

% Large () brackets on different lines of an eqnarray environment
\newcommand{\Leftbrace}[1]{\left(\raisebox{0mm}[#1][#1]{}\right.}
\newcommand{\Rightbrace}[1]{\left.\raisebox{0mm}[#1][#1]{}\right)}

% Funky symobols for footnotes
\newcommand{\symbolfootnote}{\renewcommand{\thefootnote}{\fnsymbol{footnote}}}
% now add \symbolfootnote to the beginning of the document...

\newcommand{\normallinespacing}{\renewcommand{\baselinestretch}{1.5} \normalsize}
\newcommand{\mediumlinespacing}{\renewcommand{\baselinestretch}{1.2} \normalsize}
\newcommand{\narrowlinespacing}{\renewcommand{\baselinestretch}{1.0} \normalsize}
\newcommand{\bump}{\noalign{\vspace*{\doublerulesep}}}
\newcommand{\cell}{\multicolumn{1}{}{}}
\newcommand{\spann}{\mbox{span}}
\newcommand{\diagg}{\mbox{diag}}
\newcommand{\modd}{\mbox{mod}}
\newcommand{\minn}{\mbox{min}}
\newcommand{\andd}{\mbox{and}}
\newcommand{\forr}{\mbox{for}}
\newcommand{\EE}{\mbox{E}}

\newcommand{\deff}{\stackrel{\mathrm{def}}{=}}
\newcommand{\syncc}{~\stackrel{\textstyle \rhd\kern-0.57em\lhd}{\scriptstyle L}~}

\def\coop{\mbox{\large $\rhd\!\!\!\lhd$}}
\newcommand{\sync}[1]{\raisebox{-1.0ex}{$\;\stackrel{\coop}{\scriptscriptstyle
#1}\,$}}

\newtheorem{definition}{Definition}[chapter]
\newtheorem{theorem}{Theorem}[chapter]

\newcommand{\Figref}[1]{Figure~\ref{#1}}
\newcommand{\fig}[3]{
\begin{figure}[!ht]
\begin{center}
\scalebox{#3}{\includegraphics{figs/#1.ps}}
\vspace{-0.1in}
\caption[ ]{\label{#1} #2}
\end{center}
\end{figure}
}

\newcommand{\figtwo}[8]{
\begin{figure}
\parbox[b]{#4 \textwidth}{
\begin{center}
\scalebox{#3}{\includegraphics{figs/#1.ps}}
\vspace{-0.1in}
\caption{\label{#1}#2}
\end{center}
}
\hfill
\parbox[b]{#8 \textwidth}{
\begin{center}
\scalebox{#7}{\includegraphics{figs/#5.ps}}
\vspace{-0.1in}
\caption{\label{#5}#6}
\end{center}
}
\end{figure}
}

but I don't see anything.

I am using XeLaTeX and have the following codes in preamble:

\usepackage{fontspec} % to import fonts via XeTeX
\setmainfont{CMU Serif} % TrueType font of Computer Modern
\setromanfont{CMU Serif} % Roman TrueType
\setsansfont{CMU Serif} % Sans TrueType
\setmonofont{Latin Modern Mono Prop} % Mono TrueType font

Other notes: I am using EPS files (edited in Illustrator) to embed my graphs, but I've made sure the fonts used there are TrueType as well:

UPDATE: Just wanted to update this post in case somebody else has the same problem. I followed @cfr suggestion and got rid of the CMR, Nimbus, rtxmi, txmia and txsy. Also, as @Sverre mentioned in the comments below, one of the culprits was the images I was using in my document. They were EPS files and Illustrator was embedding the font within them. So to get around that, I followed this guide and converted my images into outlines.

And now I only have these TT fonts embedded:

Answer 1

Here's a cut-down version of your preamble with some comments and a minimal set up for Latin Modern with Latin Modern Math:

\documentclass[letterpaper]{article}
\usepackage[left=1.5in,right=1in,top=1.25in,bottom=1.25in]{geometry}

\usepackage{fontspec}% to import fonts via XeTeX
% better to use Latin Modern across the board than mix with CMU, I think - LM is the default
\setmonofont{Latin Modern Mono Prop} % Mono TrueType font
\usepackage{unicode-math}

%% The following packages will all introduce type1 fonts:
% \usepackage{latexsym}
% \usepackage{txfonts}  % for upright greek letters | use $\betaup$ or $\muup$
% \usepackage{gensymb} % for degree sign \degree

%% These seem prima facie problematic based on name alone but I've no idea what is in them so can't say for sure
% \usepackage{mathchars}
% \input{icthesis.sty}

%% These are potentially problematic but I've no idea how they are defined
% \newcommand{\Prob}{\bbbp}
% \newcommand{\Real}{\bbbr}
% \newcommand{\real}{\Real}
% \newcommand{\Int}{\bbbz}
% \newcommand{\Nat}{\bbbn}

%% Do NOT use \sf, \bf, \cal etc. in LaTeX documents - these switches are long deprecated

\begin{document}
  Some text $some maths \mathcal{ab} \mathrm{roman} \mathbb{blackboard}$

\textcopyright
\end{document}

Note that textcomp is not required for things like \textcopyright with this configuration.

For Asana, add

\setmathfont{Asana Math}

which will use the .ttc.

You need to be very careful about the symbols and scripts you use in order to ensure that no type1 fonts creep in.

I would seriously ask them to clarify this requirement. If their point is that they want to insist on scalable fonts, that is entirely reasonable and an awful lot easier to implement.

And if they really don't want scalable, as they claim, then presumably they do not permit submissions prepared with word processors at all. They also can't possibly want True Type in that case. In that case, you would need to force TeX to use only MetaFont source fonts. These scale horribly in well-know PDF viewing software.