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I am compiling a document using the bioinformatics stylesheet. Compilation has been extremely slow on my local machine (64-bit quad-core i5 Lenovo x230 running Texmaker on Windows 7), and on ShareLaTeX.

Below are my raw logs from ShareLaTeX:

This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) (format=latex 2014.4.2)  21 MAY 2014 00:28
entering extended mode
 \write18 enabled.
 %&-line parsing enabled.
**document.tex
(/compile/document.tex
LaTeX2e <2011/06/27>
Babel <3.9k> and hyphenation patterns for 78 languages loaded.
(/compile/bioinfo.cls
Document Class: bioinfo 2003/02/08 0.1
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/inputenc.sty
Package: inputenc 2008/03/30 v1.1d Input encoding file
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Package: crop 2001/11/16 v1.6 cropmarks (mf)
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\CROP@index=\count79
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
) (/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/graphics.cfg
File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
)
Package graphics Info: Driver file: dvips.def on input line 91.
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/dvips.def
File: dvips.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
))
\CROP@offset=\count80
Package crop Info: Local config file crop.cfg used on input line 344.
(/usr/local/texlive/2013/texmf-dist/tex/xelatex/xetexconfig/crop.cfg))
Package crop Info: using dvips graphics driver on input line 33.
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
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Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
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)
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Package: amsmath 2013/01/14 v2.14 AMS math features
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For additional information on amsmath, use the `?' option.
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Package: amstext 2000/06/29 v2.01
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LaTeX Info: Redefining \ldots on input line 378.
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LaTeX Font Info:    Redeclaring font encoding OML on input line 566.
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LaTeX Info: Redefining \[ on input line 2665.
LaTeX Info: Redefining \] on input line 2666.
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Package: array 2008/09/09 v2.4c Tabular extension package (FMi)
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Package color Info: Driver file: dvips.def on input line 130.
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LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
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(/usr/local/texlive/2013/texmf-dist/tex/latex/natbib/natbib.sty
Package: natbib 2010/09/13 8.31b (PWD, AO)
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LaTeX Info: Redefining \cite on input line 694.
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Package: hyperref 2012/11/06 v6.83m Hypertext links for LaTeX
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Package: hobsub-hyperref 2012/05/28 v1.13 Bundle oberdiek, subset hyperref (HO)

(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty
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Package: hobsub 2012/05/28 v1.13 Construct package bundles (HO)
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Package ifluatex Info: LuaTeX not detected.
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Package ifpdf Info: pdfTeX in PDF mode is not detected.
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Package etexcmds Info: Could not find \expanded.
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Package pdftexcmds Info: LuaTeX not detected.
Package pdftexcmds Info: \pdf@primitive is available.
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Package hyperref Info: Hyper figures OFF on input line 4443.
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Package hyperref Info: Plain pages OFF on input line 4458.
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Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
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LaTeX Info: Redefining \url on input line 5041.
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Package hyperref Info: Hyper figures OFF on input line 6295.
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LaTeX Info: Redefining \ref on input line 6365.
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\Hy@abspage=\count113
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Package hyperref Message: Driver (default): hdvips.

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Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
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\openout1 = `output.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 7.
LaTeX Font Info:    ... okay on input line 7.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 7.
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LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 7.
LaTeX Font Info:    ... okay on input line 7.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 7.
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LaTeX Font Info:    ... okay on input line 7.
LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 7.
LaTeX Font Info:    ... okay on input line 7.
LaTeX Font Info:    Try loading font information for OT1+ptm on input line 7.
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/ot1ptm.fd
File: ot1ptm.fd 2001/06/04 font definitions for OT1/ptm.
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\AtBeginShipoutBox=\box36
Package hyperref Info: Link coloring OFF on input line 7.
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
Package: nameref 2012/10/27 v2.43 Cross-referencing by name of section
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LaTeX Info: Redefining \ref on input line 7.
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LaTeX Info: Redefining \nameref on input line 7.
(/compile/output.out) (/compile/output.out)
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\openout3 = `output.out'.

LaTeX Font Info:    Try loading font information for OT1+phv on input line 17.
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/ot1phv.fd
File: ot1phv.fd 2001/06/04 scalable font definitions for OT1/phv.
)
LaTeX Font Info:    Font shape `OT1/phv/bx/n' in size <9> not available
(Font)              Font shape `OT1/phv/b/n' tried instead on input line 17.
LaTeX Font Info:    Font shape `OT1/phv/bx/n' in size <10> not available
(Font)              Font shape `OT1/phv/b/n' tried instead on input line 17.
LaTeX Font Info:    Font shape `OT1/phv/bx/n' in size <8> not available
(Font)              Font shape `OT1/phv/b/n' tried instead on input line 26.

Underfull \hbox (badness 2564) in paragraph at lines 38--39
\OT1/ptm/m/n/9 (also known as the factor II mutation, or the prothrombin
 []


Underfull \hbox (badness 1688) in paragraph at lines 38--39
\OT1/ptm/m/n/9 mutation) is a genetic mutation of prothrombin (also known
 []


Underfull \hbox (badness 1910) in paragraph at lines 38--39
\OT1/ptm/m/n/9 gene. [] [[]], [] [[]]
 []

Missing character: There is no � in font ptmr7t!
Missing character: There is no � in font ptmr7t!
Missing character: There is no � in font ptmr7t!
Missing character: There is no � in font ptmr7t!
Missing character: There is no � in font ptmr7t!
Missing character: There is no � in font ptmr7t!

! LaTeX Error: Cannot determine size of graphic in Thrombin_Shot.JPG (no Boundi
ngBox).

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.45 ...ludegraphics[scale=0.1]{Thrombin_Shot.JPG}
                                                  %.jpg}
Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.

File: Thrombin_Shot.JPG Graphic file (type eps)
<Thrombin_Shot.JPG>
LaTeX Font Info:    Font shape `OT1/ptm/bx/n' in size <8> not available
(Font)              Font shape `OT1/ptm/b/n' tried instead on input line 46.

LaTeX Font Warning: Font shape `OT1/cmr/m/n' in size <6.5> not available
(Font)              size <6> substituted on input line 60.


LaTeX Font Warning: Font shape `OML/cmm/m/it' in size <6.5> not available
(Font)              size <6> substituted on input line 60.


LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <6.5> not available
(Font)              size <6> substituted on input line 60.

LaTeX Font Info:    Try loading font information for U+msa on input line 60.
(/usr/local/texlive/2013/texmf-dist/tex/latex/amsfonts/umsa.fd
File: umsa.fd 2013/01/14 v3.01 AMS symbols A
)
LaTeX Font Info:    Try loading font information for U+msb on input line 60.
(/usr/local/texlive/2013/texmf-dist/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
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LaTeX Font Info:    Try loading font information for OT1+pcr on input line 15.
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File: ot1pcr.fd 2001/06/04 font definitions for OT1/pcr.
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Underfull \hbox (badness 10000) in paragraph at lines 9--16
[]\OT1/ptm/m/n/9 J. A. HUNTINGTON.  Molecular recognition
 []


Underfull \hbox (badness 4441) in paragraph at lines 9--16
\OT1/ptm/m/n/9 mechanisms of thrombin.  \OT1/ptm/m/it/9 Journal of Thrombosis a
nd
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Underfull \hbox (badness 10000) in paragraph at lines 9--16
\OT1/ptm/m/it/9 Haemostasis\OT1/ptm/m/n/9 , 3(8):1861--1872, 2005.  ISSN 1538-
 []


Underfull \hbox (badness 4505) in paragraph at lines 9--16
\OT1/ptm/m/n/9 7836.  doi: $10 . 1111 / j . 1538-[]7836 . 2005 . 01363 . x$.  U
RL
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Overfull \hbox (38.99963pt too wide) in paragraph at lines 9--16
[][][][]\OT1/ptm/m/n/9 . 
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Missing character: There is no � in font ptmr7t!
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Missing character: There is no � in font ptmr7t!

Underfull \hbox (badness 10000) in paragraph at lines 39--46
[]\OT1/ptm/m/n/9 F. R. ROSENDAAL and P. H. REITSMA.  Genetics
 []


Underfull \hbox (badness 10000) in paragraph at lines 39--46
\OT1/ptm/m/n/9 of venous thrombosis.  \OT1/ptm/m/it/9 Journal of Thrombosis
 []


Underfull \hbox (badness 10000) in paragraph at lines 39--46
\OT1/ptm/m/it/9 and Haemostasis\OT1/ptm/m/n/9 , 7:301--304, 2009.  ISSN 1538-
 []


Underfull \hbox (badness 4505) in paragraph at lines 39--46
\OT1/ptm/m/n/9 7836.  doi: $10 . 1111 / j . 1538-[]7836 . 2009 . 03394 . x$.  U
RL
 []


Overfull \hbox (38.99963pt too wide) in paragraph at lines 39--46
[][][][]\OT1/ptm/m/n/9 . 
 []


Overfull \hbox (151.8995pt too wide) in paragraph at lines 48--55
[][][][]\OT1/ptm/m/n/9 . 
 []

)
- LAST -
Extra skip:74.19739pt
Left:471.85536pt/1.94843pt
Right:397.65797pt/1.41295pt
Output:471.85536pt
LaTeX Font Info:    Font shape `OT1/phv/bx/it' in size <8> not available
(Font)              Font shape `OT1/phv/b/it' tried instead on input line 106.
LaTeX Font Info:    Font shape `OT1/phv/b/it' in size <8> not available
(Font)              Font shape `OT1/phv/b/sl' tried instead on input line 106.

Overfull \hbox (261.0pt too wide) has occurred while \output is active
[][] 
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Overfull \vbox (1.0pt too high) has occurred while \output is active []

[1

]
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 106.
Package atveryend Info: Empty hook `AfterLastShipout' on input line 106.
(/compile/output.aux)
Package atveryend Info: Empty hook `AtVeryEndDocument' on input line 106.
Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 106.
Package rerunfilecheck Info: File `output.out' has not changed.
(rerunfilecheck)             Checksum: BC8C61E6E6CBB5188DF79026742812F5;234.

LaTeX Font Warning: Size substitutions with differences
(Font)              up to 0.5pt have occurred.

 ) 
Here is how much of TeX's memory you used:
 6861 strings out of 493309
 96910 string characters out of 6137849
 206676 words of memory out of 5000000
 10224 multiletter control sequences out of 15000+600000
 13016 words of font info for 40 fonts, out of 8000000 for 9000
 961 hyphenation exceptions out of 8191
 37i,8n,28p,4540b,364s stack positions out of 5000i,500n,10000p,200000b,80000s

Output written on /compile/output.dvi (1 page, 12836 bytes).

ShareLaTeX tells me there is a server error (though it doesn't tell me what).

2 questions:

(1) Is my code to blame for this lackadaisical speed? Everything compiled perfectly a few hours ago, with no changes.

(2) If my code is not to blame, are there any packages that would be causing this sudden change in behavior?

Code:

\documentclass{bioinfo}
\usepackage{hyperref}
\usepackage{natbib}
\copyrightyear{2005}
\usepackage{graphicx}
\pubyear{2005}
\begin{document}
\firstpage{1}

\title[Analysis of Prothrombin G20210A]{NICE SUBTITLE}
\author{Jeffrey Wubbenhorst}
%\address{$^{1}$Department of XXXXXXX, Address XXXX etc.\\
%$^{2}$Department of XXXXXXXX, Address XXXX etc.}

%\history{Received on XXXXX; revised on XXXXX; accepted on XXXXX}

\section{Contact:}\href{Jeffrey Wubbenhorst}{wubbenhorst14j@ncssm.edu}

%\maketitle

\begin{abstract}

%\section{Motivation:}
%Here is my abstract. As you may observe, it is rather sparse for the time being. 

\section{Results:}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation 

\section{Availability:}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis 

%\section{Contact:} \href{name@bio.com}{name@bio.com}
\end{abstract}

\section{Introduction}

%Discuss blood clots
Prothrombin G20210A is a genetic variant that drastically increases the probability of blood clots in the veins. Prothrombin G20210A (also known as the factor II mutation, or the prothrombin mutation) is a genetic mutation of prothrombin (also known as coagulation factor II) resulting from a single polymorphism. The mutation occurs primarily in males, and almost exclusively in Caucasians, with rougly 3\% of the population carrying the gene.  \cite{JTH3394, Rosendaal01012005} Prothrombin G20210A has also been associated with obstetric complications. \cite{Obstetric} The polymorphism occurs on the noncoding region of the prothrombin gene, replacing guanine with adenine. \cite{pmid8916933} 

Thrombin is formed from prothrombin by coming into contact with prothrombinase (also known as Factor X or thrombokinase), an enzyme in the coagulation cascade that cleaves prothrombin to form thrombin. Thrombin is a crucial part of the coagulation cascade through the conversion of various compounds, especially cleaving fibrinogen to create a fibrin clot. \cite{pmid10528826,JTH:JTH1363} 

The active and inactive forms of thrombin (from left to right) are shown below:

\begin{figure}[h!]
\includegraphics[scale=0.1]{Thrombin_Shot}%.jpg}
\caption{Active and Inactive Forms of Thrombin}
%\label{This here is a label.}
%This is a visualization in Molegro of 1MKX. 
\end{figure}

Prothrombin is encoded by the F2 gene (HGNC ID 3535), located at 11p11.2. This analysis will focus on the Prothrombin G20210A mutation in the context of a normal coagulation cascade. 


\section{Computational Approach}
%I can: 
% VIsualiz molecules using molegro or something else
%


\subsection*{Visualization}
%Equation~(\ref{eq:01}) Lorem ipsum  incididunt ut labore et dolore magna aliqua. Figure \ref{fig:02} shows that the above method  Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris.  \citealp{Boffelli03} might want to know about  nisi ut aliquip ex ea

\begin{methods}
\section{Methods}
%What can I do here? I should do some stuff with the Biology Workbench...
%I also need to use BLAST to look at the F2 gene


\end{methods}


\section{Conclusion}


\section*{Acknowledgement}
%Lorem ipsum dolor sit amet, consectetur.  \citealp{Boffelli03} might want to know about  adipisicing elit, sed do

\bibliographystyle{plainnat}
\bibliography{document}

\end{document}

Thanks for any help that can be given. Project is less than 6 pages long. BibTeX has worked perfectly.

EDIT: I commented out the only image I had just to see what would happen; ShareLaTeX now works.

share|improve this question
1  
Why are you compiling to dvi and not pdf directly? –  Juri Robl May 21 at 7:39
    
I meant to compile to pdf directly... Is there evidence I am not doing so? –  Qu0rk May 21 at 15:08
    
@Qu0rk The last line of the log: Output written on /compile/output.dvi (1 page, 12836 bytes). –  giordano May 21 at 15:24
    
You're right! I must have messed that up. –  Qu0rk May 21 at 15:37

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