Citation not working in latex using natbib package - latex

I am new to latex. I have been trying to add citations in a document but its not working. I have used the package natbib and the command \citet{DAVANZO201573} in the 2nd line of the first paragraph. The bib file name is file1.bib
I get the following error:
Package natbib Warning: Citation `DAVANZO201573' on page 1 undefined on input line 10.
Overfull \hbox (42.93008pt too wide) in paragraph at lines 10--17
\OT1/cmr/m/n/10.95 190829A. (https://fermi.gsfc.nasa.gov/science/mtgs/symposia/
2020/program/189/).
[1] [2] (./intro.bbl
! LaTeX Error: Can be used only in preamble."
Below is the content in the .tex file
\documentclass[11pt]{article}
\usepackage{placeins}
\usepackage{natbib}
\begin{document}
\section{Introduction}
Gamma ray bursts are one of the most energetic and mysterious phenomena in the universe with emissions peaking in the gamma rays detected at cosmological distances \citet{DAVANZO201573}. The duration varies from a few milli seconds to minutes detected from random locations in the sky.
\newpage
\bibliographystyle{plainnat}
\bibliography{file1}
\end{document}
The content in the bib file is:
#article{DAVANZO201573,
title = "Short gamma-ray bursts: A review",
journal = "Journal of High Energy Astrophysics",
volume = "7",
pages = "73 - 80",
year = "2015",
note = "Swift 10 Years of Discovery, a novel approach to Time Domain Astronomy",
issn = "2214-4048",
doi = "https://doi.org/10.1016/j.jheap.2015.07.002",
url = "http://www.sciencedirect.com/science/article/pii/S2214404815000415",
author = "P. D'Avanzo",
abstract = "Gamma-Ray Bursts (GRBs) are rapid, bright flashes of radiation peaking in the gamma-ray band occurring at an average rate of one event per day at cosmological distances. They are characterized by a collimated relativistic outflow pushing through the interstellar medium shining in gamma-rays powered by a central engine. This prompt phase is followed by a fading afterglow emission at longer wavelength, powered in part by the expanding outflow, and in part by continuous energy injection by the central engine. The observed evidences of supernovae associated to long GRBs (those with a duration of the gamma-ray emission >2 s) brought to a general consensus on indicating the core collapse of massive stars as the progenitor of these events. Following the most accredited model, short GRBs (the events with a duration of the gamma-ray emission ≤2 s) originate from the coalescence of compact binary systems (two neutron stars or neutron star-black hole systems). This paper presents a review of the observational properties of short GRBs and shows how the study of these properties can be used as a tool to unveil their elusive progenitors and provide information on the nature of the central engine powering the observed emission. The increasing evidence for compact object binary progenitors makes short GRBs one of the most promising sources of gravitational waves for the forthcoming Advanced LIGO/Virgo experiments."
}
Below is the output of the bibtex command:
I couldn't open file name `file1.aux'
This the .log file
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=latex 2020.5.29) 12 JUN 2020 16:02
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**intro.tex
(./intro.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo
File: size11.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
\c#part=\count79
\c#section=\count80
\c#subsection=\count81
\c#subsubsection=\count82
\c#paragraph=\count83
\c#subparagraph=\count84
\c#figure=\count85
\c#table=\count86
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(/usr/share/texlive/texmf-dist/tex/latex/placeins/placeins.sty
Package: placeins 2005/04/18 v 2.2
)
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty
Package: natbib 2010/09/13 8.31b (PWD, AO)
\bibhang=\skip43
\bibsep=\skip44
LaTeX Info: Redefining \cite on input line 694.
\c#NAT#ctr=\count87
) (./intro.aux)
\openout1 = `intro.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
Package natbib Warning: Citation `DAVANZO201573' on page 1 undefined on input l
ine 11.
LaTeX Font Info: External font `cmex10' loaded for size
(Font) <10.95> on input line 14.
LaTeX Font Info: External font `cmex10' loaded for size
(Font) <8> on input line 14.
LaTeX Font Info: External font `cmex10' loaded for size
(Font) <6> on input line 14.
Overfull \hbox (42.93008pt too wide) in paragraph at lines 11--18
\OT1/cmr/m/n/10.95 190829A. (https://fermi.gsfc.nasa.gov/science/mtgs/symposia/
2020/program/189/).
[]
[1
] [2] (./intro.bbl
! LaTeX Error: Can be used only in preamble.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.1 \documentclass
[11pt]{article}
?
! Emergency stop.
...
l.1 \documentclass
[11pt]{article}
Your command was ignored.
Type I <command> <return> to replace it with another command,
or <return> to continue without it.
Here is how much of TeX's memory you used:
582 strings out of 492983
6874 string characters out of 6134922
63861 words of memory out of 5000000
4215 multiletter control sequences out of 15000+600000
7897 words of font info for 28 fonts, out of 8000000 for 9000
1141 hyphenation exceptions out of 8191
21i,4n,22p,1264b,109s stack positions out of 5000i,500n,10000p,200000b,80000s
Output written on intro.dvi (2 pages, 5488 bytes). ```

The solution was to take the figures out of folders and put them in the root in the same place where the .tex file is.

Related

Letters and numbers in math do not use "mainfont" nor "mathfont"

I notice that, in math mode (i.e., in quarto, $$...$$ or $...), letters and numbers are being set in a default font irrespective of the mainfont or mathfont. Thus, variable names and numbers are being typeset in a different font.
mathfont does have effect on math operators, e.g. \log will be typeset using the mathfont. However, letters and numbers are not. Is this expected behavior?
I know a workaround. That is to use \mathit{} for the entire equation, then use \mathrm{} for numbers that need to be upright. Then it looks right, but it makes the coding so much more heavy (than it already may be).
Compile the following document to see the issue:
---
documentclass: article
mainfont: Lato
mathfont: Lato
---
$$ y = 123\cdot\log{x} $$
$$ \mathit{y = \mathrm{123}\cdot\log{x}} $$
(Eventually substitute your own font). The second equation looks how it ought to be. In the irst equation, only operators (log) use the mathfont. Other items use a default "latex" font (the same you have when not specifying a mainfont).
Not every font contains the necessary math symbols, Lato does not contain them. You'll see a warning like this in your .log file:
Package fontspec Warning: Font "Lato" does not contain requested Script
(fontspec) "Math".
In particular for sans serif fonts, there aren't a lot to choose from and the few which exist are often incomplete.
One sans serif font which provides a fairly good coverage is Fira Math (... but it's design might be a bit polarizing)
---
documentclass: article
mainfont: Lato
mathfont: Fira Math
format:
pdf
---
$$ y = 123\cdot\log{x} $$
$$ \mathit{y = \mathrm{123}\cdot\log{x}} $$
If you'd like to use the letters and numbers from the text font in math mode, you could use the mathastext package:
% !TeX TS-program = lualatex
\documentclass{article}
\usepackage[no-math]{fontspec}
\setmainfont{Lato}
\usepackage{mathastext}
\begin{document}
\[ y = 123\cdot\log{x} \]
\end{document}

biber and biblatex incompatible versions

I'm using Texmaker and the configuration PDFLatex > Bib(la)tex > 2x PDFLatex > View PDF for Quick Build.
But after compiling I get the following error:
INFO - This is Biber 2.17 INFO - Logfile is 'paper.blg' INFO -
Reading 'paper.bcf' ERROR - Error: Found biblatex control file
version 3.7, expected version 3.8. This means that your biber (2.17)
and biblatex (3.15a) versions are incompatible. See compat matrix in
biblatex or biber PDF documentation. INFO - ERRORS: 1
I checked the biber docs pdf and the latest compatible versions are Biber version 2.17 and Biblatex version 3.17.
Using MiKTeX Console I updated both (see images below) but TexMaker doesn't seem to care...
Any ideas on how to get it to compile it correctly?
EDIT: As requested the content of the .log-file:
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (MiKTeX 22.3) (preloaded format=pdflatex 2022.4.16) 17 APR 2022 07:55
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**./paper.tex
(paper.tex
LaTeX2e <2021-11-15> patch level 1
L3 programming layer <2022-04-10>
(C:\Program Files\MiKTeX 2.9\tex/latex/ieeetran\IEEEtran.cls
Document Class: IEEEtran 2015/08/26 V1.8b by Michael Shell
-- See the "IEEEtran_HOWTO" manual for usage information.
-- http://www.michaelshell.org/tex/ieeetran/
\#IEEEtrantmpdimenA=\dimen138
\#IEEEtrantmpdimenB=\dimen139
\#IEEEtrantmpdimenC=\dimen140
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\#IEEEtrantmptoksA=\toks16
LaTeX Font Info: Trying to load font information for OT1+ptm on input line 5
03.
(C:\Program Files\MiKTeX 2.9\tex/latex/psnfss\ot1ptm.fd
File: ot1ptm.fd 2001/06/04 font definitions for OT1/ptm.
)
-- Using 8.5in x 11in (letter) paper.
-- Using PDF output.
\#IEEEnormalsizeunitybaselineskip=\dimen141
-- This is a 10 point document.
\CLASSINFOnormalsizebaselineskip=\dimen142
\CLASSINFOnormalsizeunitybaselineskip=\dimen143
\IEEEnormaljot=\dimen144
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <5> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
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(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
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(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
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(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
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 1090.
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(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <9> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
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(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <10> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <10> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <11> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <11> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <12> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <12> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <17> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <17> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <20> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <20> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <24> not available
(Font) Font shape `OT1/ptm/b/n' tried instead on input line 1090.
LaTeX Font Info: Font shape `OT1/ptm/bx/it' in size <24> not available
(Font) Font shape `OT1/ptm/b/it' tried instead on input line 1090.
\IEEEquantizedlength=\dimen145
\IEEEquantizedlengthdiff=\dimen146
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\IEEEiedtopsep=\skip47
\c#section=\count188
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\c#paragraph=\count191
\c#IEEEsubequation=\count192
\abovecaptionskip=\skip48
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\c#figure=\count193
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\#IEEEeqnnumcols=\count195
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\#IEEEquantizeheightA=\dimen156
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\#IEEEquantizeheightC=\dimen158
\#IEEEquantizeprevdepth=\dimen159
\#IEEEquantizemultiple=\count198
\#IEEEquantizeboxA=\box50
\#IEEEtmpitemindent=\dimen160
\IEEEPARstartletwidth=\dimen161
\c#IEEEbiography=\count199
\#IEEEtranrubishbin=\box51
) (C:\Program Files\MiKTeX 2.9\tex/latex/cite\cite.sty
LaTeX Info: Redefining \cite on input line 302.
LaTeX Info: Redefining \nocite on input line 332.
Package: cite 2015/02/27 v 5.5
)
(C:\Program Files\MiKTeX 2.9\tex/latex/amsmath\amsmath.sty
Package: amsmath 2021/10/15 v2.17l AMS math features
\#mathmargin=\skip50
For additional information on amsmath, use the `?' option.
(C:\Program Files\MiKTeX 2.9\tex/latex/amsmath\amstext.sty
Package: amstext 2021/08/26 v2.01 AMS text
(C:\Program Files\MiKTeX 2.9\tex/latex/amsmath\amsgen.sty
File: amsgen.sty 1999/11/30 v2.0 generic functions
\#emptytoks=\toks17
\ex#=\dimen162
))
(C:\Program Files\MiKTeX 2.9\tex/latex/amsmath\amsbsy.sty
Package: amsbsy 1999/11/29 v1.2d Bold Symbols
\pmbraise#=\dimen163
)
(C:\Program Files\MiKTeX 2.9\tex/latex/amsmath\amsopn.sty
Package: amsopn 2021/08/26 v2.02 operator names
)
\inf#bad=\count266
LaTeX Info: Redefining \frac on input line 234.
\uproot#=\count267
\leftroot#=\count268
LaTeX Info: Redefining \overline on input line 399.
\classnum#=\count269
\DOTSCASE#=\count270
LaTeX Info: Redefining \ldots on input line 496.
LaTeX Info: Redefining \dots on input line 499.
LaTeX Info: Redefining \cdots on input line 620.
\Mathstrutbox#=\box52
\strutbox#=\box53
\big#size=\dimen164
LaTeX Font Info: Redeclaring font encoding OML on input line 743.
LaTeX Font Info: Redeclaring font encoding OMS on input line 744.
\macc#depth=\count271
\c#MaxMatrixCols=\count272
\dotsspace#=\muskip16
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\tag#help=\toks18
\row#=\count275
\column#=\count276
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\andhelp#=\toks19
\eqnshift#=\dimen165
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\tagwidth#=\dimen168
\totwidth#=\dimen169
\lineht#=\dimen170
\#envbody=\toks20
\multlinegap=\skip51
\multlinetaggap=\skip52
\mathdisplay#stack=\toks21
LaTeX Info: Redefining \[ on input line 2938.
LaTeX Info: Redefining \] on input line 2939.
)
(C:\Program Files\MiKTeX 2.9\tex/latex/amsfonts\amssymb.sty
Package: amssymb 2013/01/14 v3.01 AMS font symbols
(C:\Program Files\MiKTeX 2.9\tex/latex/amsfonts\amsfonts.sty
Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info: Redeclaring math symbol \hbar on input line 98.
LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold'
(Font) U/euf/m/n --> U/euf/b/n on input line 106.
))
(C:\Program Files\MiKTeX 2.9\tex/latex/algorithms\algorithmic.sty
Package: algorithmic 2009/08/24 v0.1 Document Style `algorithmic'
(C:\Program Files\MiKTeX 2.9\tex/latex/base\ifthen.sty
Package: ifthen 2020/11/24 v1.1c Standard LaTeX ifthen package (DPC)
)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics\keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV#toks#=\toks22
)
\c#ALC#unique=\count278
\c#ALC#line=\count279
\c#ALC#rem=\count280
\c#ALC#depth=\count281
\ALC#tlm=\skip53
\algorithmicindent=\skip54
)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics\graphicx.sty
Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics\graphics.sty
Package: graphics 2021/03/04 v1.4d Standard LaTeX Graphics (DPC,SPQR)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics\trig.sty
Package: trig 2021/08/11 v1.11 sin cos tan (DPC)
)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics-cfg\graphics.cfg
File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
)
Package graphics Info: Driver file: pdftex.def on input line 107.
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics-def\pdftex.def
File: pdftex.def 2020/10/05 v1.2a Graphics/color driver for pdftex
))
\Gin#req#height=\dimen171
\Gin#req#width=\dimen172
)
(C:\Program Files\MiKTeX 2.9\tex/latex/base\textcomp.sty
Package: textcomp 2020/02/02 v2.0n Standard LaTeX package
)
(C:\Program Files\MiKTeX 2.9\tex/latex/xcolor\xcolor.sty
Package: xcolor 2021/10/31 v2.13 LaTeX color extensions (UK)
(C:\Program Files\MiKTeX 2.9\tex/latex/graphics-cfg\color.cfg
File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package xcolor Info: Driver file: pdftex.def on input line 227.
Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1352.
Package xcolor Info: Model `hsb' substituted by `rgb' on input line 1356.
Package xcolor Info: Model `RGB' extended on input line 1368.
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Package xcolor Info: Model `Hsb' substituted by `hsb' on input line 1371.
Package xcolor Info: Model `tHsb' substituted by `hsb' on input line 1372.
Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1373.
Package xcolor Info: Model `Gray' substituted by `gray' on input line 1374.
Package xcolor Info: Model `wave' substituted by `hsb' on input line 1375.
)
(C:\Program Files\MiKTeX 2.9\tex/latex/l3backend\l3backend-pdftex.def
File: l3backend-pdftex.def 2022-04-14 L3 backend support: PDF output (pdfTeX)
\l__color_backend_stack_int=\count282
\l__pdf_internal_box=\box54
)
(paper.aux)
\openout1 = `paper.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 12.
LaTeX Font Info: ... okay on input line 12.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 12.
LaTeX Font Info: ... okay on input line 12.
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LaTeX Font Info: ... okay on input line 12.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 12.
LaTeX Font Info: ... okay on input line 12.
-- Lines per column: 56 (exact).
(C:\Program Files\MiKTeX 2.9\tex/context/base/mkii\supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count283
\scratchdimen=\dimen173
\scratchbox=\box55
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\MPnumerator=\count287
\makeMPintoPDFobject=\count288
\everyMPtoPDFconversion=\toks24
) (C:\Program Files\MiKTeX 2.9\tex/latex/epstopdf-pkg\epstopdf-base.sty
Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf
Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4
85.
(C:\Program Files\MiKTeX 2.9\tex/latex/00miktex\epstopdf-sys.cfg
File: epstopdf-sys.cfg 2021/03/18 v2.0 Configuration of epstopdf for MiKTeX
))
LaTeX Font Info: Trying to load font information for U+msa on input line 26.
(C:\Program Files\MiKTeX 2.9\tex/latex/amsfonts\umsa.fd
File: umsa.fd 2013/01/14 v3.01 AMS symbols A
)
LaTeX Font Info: Trying to load font information for U+msb on input line 26.
(C:\Program Files\MiKTeX 2.9\tex/latex/amsfonts\umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
)
LaTeX Warning: Citation `ref1' on page 1 undefined on input line 48.
(paper.bbl)
** Conference Paper **
Before submitting the final camera ready copy, remember to:
1. Manually equalize the lengths of two columns on the last page
of your paper;
2. Ensure that any PostScript and/or PDF output post-processing
uses only Type 1 fonts and that every step in the generation
process uses the appropriate paper size.
[1{C:/Users/User/AppData/Local/MiKTeX/2.9/fonts/map/pdftex/pdftex.map}
]
(paper.aux)
LaTeX Warning: There were undefined references.
)
Here is how much of TeX's memory you used:
4160 strings out of 478541
65167 string characters out of 2849516
361035 words of memory out of 3000000
22347 multiletter control sequences out of 15000+600000
507238 words of font info for 100 fonts, out of 8000000 for 9000
1141 hyphenation exceptions out of 8191
55i,8n,62p,288b,266s stack positions out of 10000i,1000n,20000p,200000b,80000s
{C:/Program Files/MiKTeX 2.9/fonts/enc/dvips/base/8r.enc}<C:/Program Files/Mi
KTeX 2.9/fonts/type1/urw/times/utmb8a.pfb><C:/Program Files/MiKTeX 2.9/fonts/ty
pe1/urw/times/utmbi8a.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/urw/times/ut
mr8a.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/urw/times/utmri8a.pfb>
Output written on paper.pdf (1 page, 56334 bytes).
PDF statistics:
27 PDF objects out of 1000 (max. 8388607)
0 named destinations out of 1000 (max. 500000)
1 words of extra memory for PDF output out of 10000 (max. 10000000)
EDIT 2: After changing biber % to bibtex % in the Commands Settings of Texmaker (I changed it based on this post), the minimal working example looks like this (eventhough the references are still empty...):
\documentclass[conference]{IEEEtran}
%\IEEEoverridecommandlockouts
% The preceding line is only needed to identify funding in the first footnote. If that is unneeded, please comment it out.
\usepackage{cite}
\usepackage{amsmath,amssymb,amsfonts}
\usepackage{algorithmic}
\usepackage{graphicx}
\usepackage{textcomp}
\usepackage{xcolor}
\def\BibTeX{{\rm B\kern-.05em{\sc i\kern-.025em b}\kern-.08em
T\kern-.1667em\lower.7ex\hbox{E}\kern-.125emX}}
\begin{document}
\title{Paper}
\author{\IEEEauthorblockN{to-do}
\IEEEauthorblockA{\textit{to-do} \\
\textit{to-do}\\
to-do\\
to-do}
}
\maketitle
\begin{abstract}
This document is a model and instructions for \LaTeX.
This and the IEEEtran.cls file define the components of your paper [title, text, heads, etc.]. *CRITICAL: Do Not Use Symbols, Special Characters, Footnotes,
or Math in Paper Title or Abstract.
\end{abstract}
\begin{IEEEkeywords}
keywords
\end{IEEEkeywords}
\section{Introduction}
This document is a model and instructions for \LaTeX.
Please observe the conference page limits. \cite{ref1}
\section*{References}
\bibliographystyle{IEEEtran}
\bibliography{refs}
\end{document}
The output pdf looks like this:

Texmaker "! Extra \endgroup." compiling error

I have installed Miktex and Texmaker and am trying to compile a very simple tex file:
\documentclass[10pt, twocolumn]{revtex4}
\begin{document}
hello
\end{document}
but I am getting the error on the \begin{document} line "!Extra\endgroup.\document->\endgroup\init#documenthook\set#typesize#hook\normalsize\set... \begin{document}". The error: image .The pdf shows:latex pdf
Here is the .log file:
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (MiKTeX 20.12) (preloaded format=pdflatex 2021.1.16) 16 JAN 2021 17:56
entering extended mode
**./test_2.tex
(test_2.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(E:\Miktex\tex/latex/revtex4\revtex4.cls
Document Class: revtex4 2001/08/03 v4.0 (http://publish.aps.org/revtex4/ for do
cumentation)
Copyright (c) 2001 The American Physical Society.
mailto:revtex#aps.org
Licensed under the LPPL:
http://www.ctan.org/tex-archive/macros/latex/base/lppl.txt
Arthur Ogawa <ogawa#teleport.com>
Based on work by David Carlisle <david#dcarlisle.demon.co.uk>.
ltxutil: portions licensed from W. E. Baxter (web#superscript.com)
Class revtex4 Info: Repairing broken LateX \#sect on input line 596.
\intertabularlinepenalty=\count177
\#tbpen=\count178
\#arstrutbox#hline=\box47
Class revtex4 Info: Repairing broken LaTeX \#xbitor on input line 1610.
ltxgrid: portions licensed from W. E. Baxter (web#superscript.com)
\c#linecount=\count179
\output=\toks15
\#protection#box=\box48
\#topmark#saved=\toks16
\footins#saved=\box49
\pagesofar=\box50
\footbox=\box51
\pagegrid#col=\count180
Class revtex4 Info: Incorporating package {textcase} [1998/11/12 v0.06 Text on
ly upper/lower case changing (DPC)]. on input line 3682.
(E:\Miktex\tex/latex/url\url.sty
\Urlmuskip=\muskip16
Package: url 2013/09/16 ver 3.4 Verb mode for urls, etc.
)
\c#affil=\count181
\absbox=\box52
\c#part=\count182
\c#section=\count183
\c#subsection=\count184
\c#subsubsection=\count185
\c#paragraph=\count186
\c#subparagraph=\count187
\abovecaptionskip=\skip47
\belowcaptionskip=\skip48
\c#figure=\count188
\c#table=\count189
(E:\Miktex\tex/latex/natbib\natbib.sty
Package: natbib 2010/09/13 8.31b (PWD, AO)
\bibhang=\skip49
\bibsep=\skip50
LaTeX Info: Redefining \cite on input line 694.
\c#NAT#ctr=\count190
)
\widetext#top=\box53
\widetext#bot=\box54
(E:\Miktex\tex/latex/revtex4\revsymb.sty
Package: revsymb 2001/08/03 v4.0 (http://publish.aps.org/revtex4/ for documenta
tion)
LaTeX Info: Redefining \REV#mathfrak on input line 118.
))
Class revtex4 Warning: No Society specified, using generic APS style.
(E:\Miktex\tex/latex/revtex4\aps.rtx
File: aps.rtx 2001/08/03 v4.0 (http://publish.aps.org/revtex4/ for documentatio
n)
) (E:\Miktex\tex/latex/revtex4\10pt.rtx
File: 10pt.rtx 2001/08/03 v4.0 (http://publish.aps.org/revtex4/ for documentati
on)
)
! Extra \endgroup.
\document ->\endgroup
\init#documenthook \set#typesize#hook \normalsize \set...
l.2 \begin{document}
Things are pretty mixed up, but I think the worst is over.
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.2 \begin{document}
You're in trouble here. Try typing <return> to proceed.
If that doesn't work, type X <return> to quit.
(E:\Miktex\tex/latex/l3backend\l3backend-pdftex.def
File: l3backend-pdftex.def 2021-01-09 L3 backend support: PDF output (pdfTeX)
\l__kernel_color_stack_int=\count191
\l__pdf_internal_box=\box55
) (test_2.aux)
\openout1 = `test_2.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 2.
LaTeX Font Info: ... okay on input line 2.
Class revtex4 Info: Unrecognized LaTeX tabular. Please update this document cla
ss! (Proceeding with fingers crossed.) on input line 2.
Class revtex4 Info: cite was not loaded (OK!) on input line 2.
Class revtex4 Info: multicol was not loaded (OK!) on input line 2.
[1{C:/Users/l04sa/AppData/Local/MiKTeX/pdftex/config/pdftex.map}] (test_2.aux)
)
Here is how much of TeX's memory you used:
1949 strings out of 479618
26287 string characters out of 2881546
304780 words of memory out of 3000000
19187 multiletter control sequences out of 15000+200000
403430 words of font info for 27 fonts, out of 3000000 for 9000
1141 hyphenation exceptions out of 8191
53i,4n,60p,192b,111s stack positions out of 5000i,500n,10000p,200000b,50000s
<E:/Miktex/fonts/type1/public/amsfonts/cm/cmr10.pfb>
Output written on test_2.pdf (1 page, 13928 bytes).
PDF statistics:
10 PDF objects out of 1000 (max. 8388607)
0 named destinations out of 1000 (max. 500000)
1 words of extra memory for PDF output out of 10000 (max. 10000000)
I am really not sure why I am getting this, would appreciate any help. Let me know if you need more info on my setup. Thank you

pdflatex: \includegraphics{} -> file not found

first of all: I know this question is out there hundreds and thousands of times. But none of the given answers I found during the last four hours solved my specific problem and I am getting crazy here. I would be extremely grateful for any help and advice!
Trying to compile a very simple .tex file including an \includegraphics command, I end up getting a "file not found" error. Take the following as a very minimalistic example:
\documentclass{report}
\usepackage{graphicx}
\begin{document}
\includegraphics{b}
\end{document}
The image file is actually just called "b.jpg" (meanwhile), and it's definitely sitting in the same path as the tex-file. Adding ".jpg" to the command does not change a thing. Neither does calling graphics instead of graphicx.
The output file created contains the following:
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (MiKTeX 2.9.7200 64-bit) (preloaded format=pdflatex 2019.10.6) 6 OCT 2019 17:25 entering extended mode
**"C:/Neuer Ordner/test.tex" ("C:/Neuer Ordner/test.tex" LaTeX2e <2018-12-01> ("C:\Program Files\MiKTeX 2.9\tex/latex/base\article.cls" Document Class: article 2019/08/27 v1.4j Standard LaTeX document class ("C:\Program Files\MiKTeX 2.9\tex/latex/base\size10.clo" File: size10.clo 2019/08/27 v1.4j Standard LaTeX file (size option) ) \c#part=\count80 \c#section=\count81 \c#subsection=\count82 \c#subsubsection=\count83 \c#paragraph=\count84 \c#subparagraph=\count85 \c#figure=\count86 \c#table=\count87 \abovecaptionskip=\skip41 \belowcaptionskip=\skip42 \bibindent=\dimen102 ) ("C:\Program Files\MiKTeX
2.9\tex/latex/graphics\graphics.sty" Package: graphics 2019/07/20 v1.3b Standard LaTeX Graphics (DPC,SPQR)
("C:\Program Files\MiKTeX 2.9\tex/latex/graphics\trig.sty" Package: trig 2016/01/03 v1.10 sin cos tan (DPC) ) ("C:\Program Files\MiKTeX
2.9\tex/latex/graphics-cfg\graphics.cfg" File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration ) Package graphics Info: Driver file: pdftex.def on input line 105.
("C:\Program Files\MiKTeX 2.9\tex/latex/graphics-def\pdftex.def" File: pdftex.def 2018/01/08 v1.0l Graphics/color driver for pdftex )) (test.aux) \openout1 = `test.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line
4. LaTeX Font Info: ... okay on input line 4. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 4. LaTeX Font Info: ... okay on input line 4. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 4. LaTeX Font Info: ... okay on input line 4. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 4. LaTeX Font Info: ... okay on input line 4. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 4. LaTeX Font Info: ... okay on input line 4. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 4. LaTeX Font Info: ... okay on input line 4.
(C:\Users\rB\AppData\Roaming\MiKTeX\2.9\tex/context/base/mkii\supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count88 \scratchdimen=\dimen103 \scratchbox=\box27 \nofMPsegments=\count89 \nofMParguments=\count90 \everyMPshowfont=\toks14 \MPscratchCnt=\count91 \MPscratchDim=\dimen104 \MPnumerator=\count92 \makeMPintoPDFobject=\count93 \everyMPtoPDFconversion=\toks15 ) ("C:\Program Files\MiKTeX 2.9\tex/latex/oberdiek\epstopdf-base.sty" Package: epstopdf-base 2016/05/15 v2.6 Base part for package epstopdf
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\infwarerr.sty" Package: infwarerr 2016/05/16 v1.4 Providing info/warning/error messages (HO) ) ("C:\Program Files\MiKTeX
2.9\tex/latex/oberdiek\grfext.sty" Package: grfext 2016/05/16 v1.2 Manage graphics extensions (HO)
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\kvdefinekeys.sty" Package: kvdefinekeys 2016/05/16 v1.4 Define keys (HO)
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\ltxcmds.sty" Package: ltxcmds 2016/05/16 v1.23 LaTeX kernel commands for general use (HO) ))) ("C:\Program Files\MiKTeX
2.9\tex/latex/oberdiek\kvoptions.sty" Package: kvoptions 2016/05/16 v3.12 Key value format for package options (HO)
("C:\Program Files\MiKTeX 2.9\tex/latex/graphics\keyval.sty" Package: keyval 2014/10/28 v1.15 key=value parser (DPC) \KV#toks#=\toks16 ) ("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\kvsetkeys.sty" Package: kvsetkeys 2016/05/16 v1.17 Key value parser (HO)
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\etexcmds.sty" Package: etexcmds 2016/05/16 v1.6 Avoid name clashes with e-TeX commands (HO)
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\ifluatex.sty" Package: ifluatex 2016/05/16 v1.4 Provides the ifluatex switch (HO) Package ifluatex Info: LuaTeX not detected. )))) ("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\pdftexcmds.sty" Package: pdftexcmds 2019/07/25 v0.30 Utility functions of pdfTeX for LuaTeX (HO )
("C:\Program Files\MiKTeX 2.9\tex/generic/oberdiek\ifpdf.sty" Package: ifpdf 2018/09/07 v3.3 Provides the ifpdf switch ) Package pdftexcmds Info: LuaTeX not detected. Package pdftexcmds Info: \pdf#primitive is available. Package pdftexcmds Info: \pdf#ifprimitive is available. Package pdftexcmds Info: \pdfdraftmode found. ) Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4
38. Package grfext Info: Graphics extension search list: (grfext) [.pdf,.png,.jpg,.mps,.jpeg,.jbig2,.jb2,.PDF,.PNG,.JPG,.JPE G,.JBIG2,.JB2,.eps] (grfext) \AppendGraphicsExtensions on input line 456. ) ! Undefined control sequence. \Ginclude#graphics ...\Ginput#path \set#curr#file
{#1}\edef \uq#curr#file {\... l.5 \includegraphics{b}
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. \Ginclude#graphics ...e \expandafter {\#curr#file
}}\expandafter \filename#p... l.5 \includegraphics{b}
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. <recently read> \unquote#name
l.5 \includegraphics{b}
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. <recently read> \quote#name
l.5 \includegraphics{b}
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. <recently read> \quote#name
l.5 \includegraphics{b}
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.
! LaTeX Error: File `b' not found.
See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ...
l.5 \includegraphics{b}
I could not locate the file with any of these extensions: .pdf,.png,.jpg,.mps,.jpeg,.jbig2,.jb2,.PDF,.PNG,.JPG,.JPEG,.JBIG2,.JB2,.eps Try typing <return> to proceed. If that doesn't work, type X <return> to quit.
[1
{C:/Users/rB/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}] (test.aux) ) Here is how much of TeX's memory you used: 1367 strings out of 492895 19199 string characters out of 3133488 80095 words of memory out of 3000000 5293 multiletter control sequences out of 15000+200000 3640 words of font info for 14 fonts, out of 3000000 for 9000 1141 hyphenation exceptions out of 8191 41i,4n,25p,289b,107s stack positions out of 5000i,500n,10000p,200000b,50000s <C :/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on test.pdf (1 page, 10121 bytes). PDF statistics: 10 PDF objects out of 1000 (max. 8388607) 0 named destinations out of 1000 (max. 500000) 1 words of extra memory for PDF output out of 10000 (max. 10000000)
Why does it begin with "This is pdfTeX", even though I explicitly chose pdflatex? Might this be the key here?
I am using pdflatex in TeXnicCenter 2.02 with MikTex 2.9 in Win10 64bit. Already tried reinstalling MikTex.
Thanks in advance for any help, it's highly appreciated!
Have you tried adding \graphicspath{{./}} to your preamble after you import graphicx? What this does is it makes the images in the same directory of the .tex file to your document to use. Afterwards, you can call \includegraphics{b.jpg} where you want to add your image.
Code example:
\documentclass{article}
\usepackage{graphicx} % Used for adding images
\graphicspath{{./}} % Import images in the same folder as this .tex file
\begin{document} % Official beginning of the document.
\includegraphics[width=\textwidth]{b.jpg}
\end{document}

"Error Producing PDF" when markdown contains a horizontal rule: --- or ***

When my Markdown file contains a horizontal rule --- or *** I receive an error regarding \Linethickness -> \Protect
I understand there have been issues with MiKTeX recently, however I am unsure whether they apply here.
I have been experiencing this issue since yesterday morning, when I was playing around trying to get the Lato font package to work with a set of Markdown files I need to convert to PDF. It had been working fine (asides from the font issue).
This could have happened when I updated MiKTeX, although at the time I hadn't realised that could be the case, as I was also playing with the templates, YAML, PS Script etc.
Since then I've been reading about the MiKTeX issue and I've tried further updates, updating package database, building formats, refreshing file name database and uninstalling and reinstalling. I have read the background in the comments section on GitHub but the suggestions there do not seem to have solved it for me, whereas they have for others.
This makes me question whether this is related, but I am relatively new to Tex, Markdown etc.
The original file was longer and more complex, but this Markdown
# Sample File
Test Test Test
---
Produces the same error
Error producing PDF.
! Missing number, treated as zero.
<to be read again>
\protect
\linethickness ->\protect
\linethickness
\setlength #1#2->#1 #2
\relax
\#rule ...#tempdimb {#2}\setlength \#tempdimc {#3}
\advance \#tempdimc \#temp...
l.362 ...nter}\rule{0.5\linewidth}{\linethickness}
Removing the --- allows the pdf to generate in both the above example and my more complex markdown file, even with templates.
I am unsure if linethickness is within the graphics package, when I look at package information I can't see anything that obviously indicates it is.
I would simply remove the offending lines but they are used throughout the remainder of the markdown files and I would prefer to find a fix, with your help, if possible!
Please could you let me know if I'm barking up the wrong tree with this recent MiKTeX issue or not, and if not, where I might be going wrong.
Many Thanks in advance.
Update:
I ran this command
pandoc -s sample.md -o sample.tex
to produce this tex:
% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
\usepackage{unicode-math}
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
\usepackage[]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\makeatletter
\#ifundefined{KOMAClassName}{% if non-KOMA class
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
\KOMAoptions{parskip=half}}
\makeatother
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\hypersetup{
hidelinks,
pdfcreator={LaTeX via pandoc}}
\urlstyle{same} % disable monospaced font for URLs
\usepackage[margin=1cm]{geometry}
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\date{}
\begin{document}
\setcounter{errorcontextlines}{40}
\hypertarget{sample-file}{%
\section{Sample File}\label{sample-file}}
Test Test Test
\begin{center}\rule{0.5\linewidth}{\linethickness}\end{center}
\end{document}
meanwhile, I tried this (as root in a latest RStudio Debian install):
~# sed 's,\\linethickness,0.5000000000pt,g' < pandoc/pandoc > /usr/lib/rstudio-server/bin/pandoc/pandoc
where the 1st pandoc/pandoc is a copy of the original from package. That keeps the same string length and valid number so that the binary won't break. That writes the hrule as:
\begin{center}\rule{0.5\linewidth}{0.5000000000pt}\end{center}
and MiKTeX seems fine with it (at least TeXworks compiles the pdf).
HTH
bye

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