所以我遇到的问题是，我的 .tex 文件的输出 pdf 的编码在某种程度上是自定义的。这是我的 tex 文件的开头：
\documentclass[a4paper,12pt]{article}
\usepackage[a4paper,margin=1in]{geometry}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage{longtable}
\usepackage{graphicx}
\usepackage{subfig}
\usepackage{listings}
\usepackage{verbatim}
\usepackage{multirow}
\usepackage{url}
\usepackage{grffile}
\usepackage[superscript]{cite}
\usepackage{calc}
\newcommand{\UnderscoreCommands}{\do\IfFileExists \do\verbatiminput%
\do\verbatimtabinput \do\citeNP \do\citeA \do\citeANP \do\citeN%
\do\shortcite \do\shortciteNP \do\shortciteA \do\shortciteANP%
\do\shortciteN \do\citeyear \do\citeyearNP%
}
\usepackage[strings]{underscore}
\usepackage{fancyhdr}
\usepackage{hyperref}
\usepackage{minted}
\addtolength{\oddsidemargin}{-5mm}
\addtolength{\evensidemargin}{-5mm}
\addtolength{\textwidth}{10mm}
\addtolength{\topmargin}{-5mm}
\addtolength{\textheight}{10mm}
\setlength{\tabcolsep}{20pt}
\renewcommand{\arraystretch}{1.3}
\renewcommand{\familydefault}{\sfdefault}
\pagestyle{fancy}
\setlength{\headheight}{15.2pt}
\newlength{\myheight}
\fancyhf{}
\fancyhead[LE,RO]{\thepage}
\fancyhead[LO,RE]{\textit{\nouppercase{\leftmark}}}
\bibliographystyle{plain}
\begin{document}
\section{Introduction}
\label{sec:intro}
We will be using a subset of a publicly available RNA-Seq
study~\cite{liu14} (the dataset is deposited in the NCBI GEO database
under accession
\href{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51403}{GSE51403}).
The dataset represents whole transcriptome sequencing of MCF7 cell line with
and without 17 beta-estradiol treatment sequenced using polyA capture and random
priming (single-end reads, 50 bp long).
cummeRbund is a convenient R-package for visualizing your RNA-Seq data. cummeRbund assumes that reads have been aligned and that the Cufflinks suite (http://Cufflinks.cbcb.umd.edu/index.html) has been used for transcript deconvolution and (if appropriate) differential expression analysis. Due to time constraints, we will not run Cufflinks during the course. More details on how to run tophat and Cufflinks can be found at the end this document. cummeRbund is a visualization package for RNA-Seq data that was designed to help you navigate through the large amount of data produced from Cufflinks transcript assembly and Cuffdiff differential expression analysis. Such analyses typically result in a large number of inter-related files that are not intuitive to navigate through. cummeRbund helps promote rapid analysis of these files by aggregating and indexing them and allows you to easily visualize and create publication-ready figures of your RNA-Seq data while maintaining appropriate relationships between connected data points.
cummeRbund starts with re-organizing output files of a Cuffdiff analysis and storing these data in a local SQLite database. cummeRbund indexes the data to speed up access to specific feature data (genes, isoforms, TSS, CDS, etc.) and preserves relationships between these features. Access to data elements is managed via the RSQLite package and data are presented in appropriately structured R classes with various convenience functions designed to streamline your workflow. This persistent database storage means that inter-connected expression values are rapidly accessible and quickly searchable in future analyses.
See more at: \url{http://compbio.mit.edu/cummeRbund/manual_2_0.html#tth_sEc2}
\end{document}
好的副本：
We will be using a subset of a publicly available RNA-Seq study
错误副本：
❲❡ ✇✐❧❧ ❜❡ ✉s✐♥❣ ❛ s✉❜s❡t ♦❢ ❛ ♣✉❜❧✐❝❧2 ❛✈❛✐❧❛❜❧❡ ❘◆❆✲❙❡q st✉❞2
原因：
\usepackage[T1]{fontenc}
解决方式：
%\usepackage[T1]{fontenc}
但实际上有时我确实需要这种编码，有没有什么办法可以解决这个问题？谢谢！
。日志档案：
Here is how much of TeX's memory you used:
9879 strings out of 495032
147712 string characters out of 6181718
243128 words of memory out of 5000000
12884 multiletter control sequences out of 15000+600000
17552 words of font info for 41 fonts, out of 8000000 for 9000
14 hyphenation exceptions out of 8191
44i,11n,43p,1053b,564s stack positions out of 5000i,500n,10000p,200000b,80000s
</home/sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecit1000.600pk>
</home/sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1000.600pk> <
/home/sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecsi1200.600pk> </h
ome/sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1200.600pk> </hom
e/sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1440.600pk> </home/
sajvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk> </home/sa
jvanderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecss0800.600pk> </home/sajv
anderzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecss1200.600pk> </home/sajvan
derzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1728.600pk> </home/sajvande
rzeeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecss1000.600pk> </home/sajvanderz
eeuw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecss2074.600pk> </home/sajvanderzee
uw/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecss1440.600pk></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmsy10.pfb>
Output written on handout_02.pdf (7 pages, 191077 bytes).
PDF statistics:
580 PDF objects out of 1000 (max. 8388607)
38 named destinations out of 1000 (max. 500000)
65 words of extra memory for PDF output out of 10000 (max. 10000000)