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I am trying to compile some tex files into pdf files using pdflatex but it is not working. Can anyone spot what the problem is? I appreciate any kind of help. I was first trying using R but it seems that the problem is with pdflatex itself.

I just used:

pdflatex TcCLB50345390.tex

This is the error log:

This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit) (preloaded format=pdflatex 2017.12.7)  7 DEC 2017 17:11
entering extended mode
**./TcCLB50345390.tex
(TcCLB50345390.tex
LaTeX2e <2017-04-15>
Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\article.cls"
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\size10.clo"
File: size10.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
)
(C:\Users\tiago\AppData\Roaming\MiKTeX\2.9\tex\latex\texshade\texshade.sty
Package: texshade 2011/05/13 LaTeX TeXshade (v1.24)

Package `texshade', Version 1.24 of 2011/12/01.
("C:\Program Files\MiKTeX 2.9\tex\latex\graphics\color.sty"
Package: color 2016/07/10 v1.1e Standard LaTeX Color (DPC)

("C:\Program Files\MiKTeX 2.9\tex\latex\graphics-cfg\color.cfg"
File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package color Info: Driver file: dvips.def on input line 147.

("C:\Program Files\MiKTeX 2.9\tex\latex\graphics-def\dvips.def"
File: dvips.def 2017/06/20 v3.1d Graphics/color driver for dvips
)
("C:\Program Files\MiKTeX 2.9\tex\latex\graphics\dvipsnam.def"
File: dvipsnam.def 2016/06/17 v3.0m Driver-dependent file (DPC,SPQR)
))
("C:\Program Files\MiKTeX 2.9\tex\latex\graphics\graphics.sty"
Package: graphics 2017/06/25 v1.2c 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 99.

("C:\Program Files\MiKTeX 2.9\tex\latex\graphics-def\pdftex.def"
File: pdftex.def 2017/06/24 v1.0g Graphics/color driver for pdftex
))
\structurefile=\read1
\featurefile=\write3
\alignfile=\read2
\sublogofile=\read3
\exp@rtfile=\write4

("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
\@emptytoks=\toks14
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
))
\symalphahelix=\mathgroup6
\loopcount=\count87
\innerloopcount=\count88
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\seq@count=\count90
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\pos@count=\count95
\res@perline=\count96
\end@count=\count97
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\pos@sum=\count103
\box@width=\skip43
\name@width=\skip44
\box@depth=\skip45
\width@tmp=\skip46
\box@height=\skip47
\number@width=\skip48
\line@stretch=\skip49
\center@fill=\skip50
\arrow@width=\skip51
\arrow@height=\skip52
\rule@thick=\skip53
\arrow@thick=\skip54
\logo@height=\skip55
\equal@width=\skip56
\equal@tmp=\skip57
\equal@height=\skip58
\temp@@length=\skip59
\vspace@legend=\skip60
\hspace@legend=\skip61
Package color Info: Redefining color LightGray on input line 1704.
Package color Info: Redefining color LightLightGray on input line 1805.
Package color Info: Redefining color LightLightLightGray on input line 1907.
)
No file TcCLB50345390.aux.
\openout1 = `TcCLB50345390.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 24.
LaTeX Font Info:    ... okay on input line 24.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 24.
LaTeX Font Info:    ... okay on input line 24.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 24.
LaTeX Font Info:    ... okay on input line 24.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 24.
LaTeX Font Info:    ... okay on input line 24.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 24.
LaTeX Font Info:    ... okay on input line 24.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 24.
LaTeX Font Info:    ... okay on input line 24.
(C:\Users\tiago\AppData\Roaming\MiKTeX\2.9\tex\context\base\supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count104
\scratchdimen=\dimen103
\scratchbox=\box26
\nofMPsegments=\count105
\nofMParguments=\count106
\everyMPshowfont=\toks15
\MPscratchCnt=\count107
\MPscratchDim=\dimen104
\MPnumerator=\count108
\makeMPintoPDFobject=\count109
\everyMPtoPDFconversion=\toks16
) ("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)

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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@=\toks17
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Package: kvsetkeys 2016/05/16 v1.17 Key value parser (HO)

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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.
)
Package etexcmds Info: Could not find \expanded.
(etexcmds)             That can mean that you are not using pdfTeX 1.50 or
(etexcmds)             that some package has redefined \expanded.
(etexcmds)             In the latter case, load this package earlier.
)))
("C:\Program Files\MiKTeX 2.9\tex\generic\oberdiek\pdftexcmds.sty"
Package: pdftexcmds 2017/03/19 v0.25 Utility functions of pdfTeX for LuaTeX (HO
)

("C:\Program Files\MiKTeX 2.9\tex\generic\oberdiek\ifpdf.sty"
Package: ifpdf 2017/03/15 v3.2 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.
)
(C:/Users/tiago/AppData/Local/Temp/Rtmp4KSpsc/seq35082e2523e2.fasta: . . . . .
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Non-PDF special ignored!

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! TeX capacity exceeded, sorry [input stack size=5000].
<to be read again> 
                   \current@color 
l.37 \end{texshade}

If you really absolutely need more capacity,
you can ask a wizard to enlarge me.


Here is how much of TeX's memory you used:
 6659 strings out of 493312
 77084 string characters out of 3138899
 293316 words of memory out of 3000000
 10209 multiletter control sequences out of 15000+200000
 4281 words of font info for 17 fonts, out of 3000000 for 9000
 1141 hyphenation exceptions out of 8191
 5000i,5n,57p,431b,1310s stack positions out of 5000i,500n,10000p,200000b,50000s
!  ==> Fatal error occurred, no output PDF file produced!
  • Welcome. The problem is that the document is "too large" (some operation eats up the TeX memory). – TeXnician Dec 7 '17 at 19:32
  • There is any way to increase TeX memory? – Tiago Bruno Dec 7 '17 at 19:39
  • You were completely right. I used a really small file as test and worked normally. Can I overcome the issue to print the big files? – Tiago Bruno Dec 7 '17 at 19:44
  • You might try LuaLaTeX. Or maybe search this site, we already have similar questions. – TeXnician Dec 7 '17 at 19:46
  • input stack overflows normally indicate a bug in the code. – Ulrike Fischer Dec 7 '17 at 20:04
0

I Found the origin of the problem. The text file was too big. Bigger than the size of the page. That was causing a fatal error.

  • That normally isn't an issue. You might have had an i. e. parbox, which was too large and always went to the next page. A thing that normally shouldn't happen. Please elaborate what the error was and expand your answer. – MaestroGlanz Jan 2 at 9:18

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