Sstrhsrtj

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 FilesMiKTeX 2.9texlatexbasearticle.cls"

Document Class: article 2014/09/29 v1.4h Standard LaTeX document class

("C:Program FilesMiKTeX 2.9texlatexbasesize10.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:UserstiagoAppDataRoamingMiKTeX2.9texlatextexshadetexshade.sty

Package: texshade 2011/05/13 LaTeX TeXshade (v1.24)



Package `texshade', Version 1.24 of 2011/12/01.

("C:Program FilesMiKTeX 2.9texlatexgraphicscolor.sty"

Package: color 2016/07/10 v1.1e Standard LaTeX Color (DPC)



("C:Program FilesMiKTeX 2.9texlatexgraphics-cfgcolor.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 FilesMiKTeX 2.9texlatexgraphics-defdvips.def"

File: dvips.def 2017/06/20 v3.1d Graphics/color driver for dvips

)

("C:Program FilesMiKTeX 2.9texlatexgraphicsdvipsnam.def"

File: dvipsnam.def 2016/06/17 v3.0m Driver-dependent file (DPC,SPQR)

))

("C:Program FilesMiKTeX 2.9texlatexgraphicsgraphics.sty"

Package: graphics 2017/06/25 v1.2c Standard LaTeX Graphics (DPC,SPQR)



("C:Program FilesMiKTeX 2.9texlatexgraphicstrig.sty"

Package: trig 2016/01/03 v1.10 sin cos tan (DPC)

)

("C:Program FilesMiKTeX 2.9texlatexgraphics-cfggraphics.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 FilesMiKTeX 2.9texlatexgraphics-defpdftex.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 FilesMiKTeX 2.9texlatexamsfontsamssymb.sty"

Package: amssymb 2013/01/14 v3.01 AMS font symbols



("C:Program FilesMiKTeX 2.9texlatexamsfontsamsfonts.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

outerloopcount=count89

seq@count=count90

killseq@count=count91

seq@percent=count92

res@count=count93

seq@pointer=count94

pos@count=count95

res@perline=count96

end@count=count97

cons@count=count98

total@count=count99

temp@count=count100

triple@count=count101

temp@@count=count102

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:UserstiagoAppDataRoamingMiKTeX2.9texcontextbasesupp-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 FilesMiKTeX 2.9texlatexoberdiekepstopdf-base.sty"

Package: epstopdf-base 2016/05/15 v2.6 Base part for package epstopdf



("C:Program FilesMiKTeX 2.9texgenericoberdiekinfwarerr.sty"

Package: infwarerr 2016/05/16 v1.4 Providing info/warning/error messages (HO)

)

("C:Program FilesMiKTeX 2.9texlatexoberdiekgrfext.sty"

Package: grfext 2016/05/16 v1.2 Manage graphics extensions (HO)



("C:Program FilesMiKTeX 2.9texgenericoberdiekkvdefinekeys.sty"

Package: kvdefinekeys 2016/05/16 v1.4 Define keys (HO)



("C:Program FilesMiKTeX 2.9texgenericoberdiekltxcmds.sty"

Package: ltxcmds 2016/05/16 v1.23 LaTeX kernel commands for general use (HO)

)))

("C:Program FilesMiKTeX 2.9texlatexoberdiekkvoptions.sty"

Package: kvoptions 2016/05/16 v3.12 Key value format for package options (HO)



("C:Program FilesMiKTeX 2.9texlatexgraphicskeyval.sty"

Package: keyval 2014/10/28 v1.15 key=value parser (DPC)

KV@toks@=toks17

)

("C:Program FilesMiKTeX 2.9texgenericoberdiekkvsetkeys.sty"

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



("C:Program FilesMiKTeX 2.9texgenericoberdieketexcmds.sty"

Package: etexcmds 2016/05/16 v1.6 Avoid name clashes with e-TeX commands (HO)



("C:Program FilesMiKTeX 2.9texgenericoberdiekifluatex.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 FilesMiKTeX 2.9texgenericoberdiekpdftexcmds.sty"

Package: pdftexcmds 2017/03/19 v0.25 Utility functions of pdfTeX for LuaTeX (HO

)



("C:Program FilesMiKTeX 2.9texgenericoberdiekifpdf.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: . . . . .

. . . . . . . . [1

Non-PDF special ignored!



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. . . [361] . . . . . . . . . . . [362] . . . . . . . . . . . [363] . . . . .

. . . . . . [364] . . . . . . . . . . . [365] . . . . . . . . . . . [366] . .

. . . . . . . . . [367] . . . . . . . . . . . [368] . . . . . . . . . . .

[369] . . . . . . . . . . . [370] . . . . . . . . . . . [371] . . . . . . . .

. . . [372] . . . . . . . . . . . [373] . . . . . . . . . . . [374] . . . . .

. . . . . . [375] . . . . . . . . . . . [376] . . . . . . . . . . . [377] . .

. . . . . . . . . [378] . . . . . . . . . . . [379] . . . . . . . . . . .

[380] . . . . . . . . . . . [381] . . . . . . . . . . . [382] . . . . . . . .

. . . [383] . . . . . . . . . . . [384] . . . . . . . . . . . [385] . . . . .

. . . . . . [386] . . . . . . . . . . . [387] . . . . . . . . . . . [388] . .

. . . . . . . . . [389] . . . . . . . . . . . [390] . . . . . . . . . . .

[391] . . . . . . . . . . . [392] . . . . . . . . . . . [393] . . . . . . . .

. . . [394] . . . . . . . . . . . [395] . . . . . . . . . . . [396] . . . . .

. . . . . . [397] . . . . . . . . . . . [398] . . . . . . . . . . . [399] . .

. . . . . . . . . [400] . . . . . . . . . . . [401] . . . . . . . . . . .

[402] . . . . . . . . . . . [403] . . . . . . . . . . . [404] . . . . . . . .

. . . [405] . . . . . . . . . . . [406] . . . . . . . . . . . [407] . . . . .

. . . . . . [408] . . . . . . . . . . . [409] . . . . . . . . . . . [410] . .

. . . . . . . . . [411] . . . . . . . . . . . [412] . . . . . . . . . . .

[413] . . . . . . . . . . . [414] . . . . . . . . . . . [415] . . . . . . . .

. . . [416] . . . . . . . . . . . [417] . . . . . . . . . . . [418] . . . . .

. . . . . . [419] . . . . . . . . . . . [420] . . . . . . . . . . . [421] . .

. . . . . . . . . [422] . . . . . . . . . . . [423] . . . . . . . . . . .

[424] . . . . . . . . . . . [425] . . . . . . . . . . . [426] . . . . . . . .

. . . [427] . . . . . . . . . . . [428] . . . . . . . . . . . [429] . . . . .

. . . . . . [430] . . . . . . . . . . . [431] . . . . . . . . . . . [432] . .

. . . . . . . . . [433] . . . . . . . . . . . [434] . . . . . . . . . . .

[435] . . . . . . . . . . . [436] . . . . . . . . . . . [437] . . . . . . . .

. . . [438] . . . . . . . . . . . [439] . . . . . . . . . . . [440] . . . . .

. . . . . . [441] . . . . . . . . . . . [442] . . . . . . . . . . . [443] . .

. . . . . . . . . [444] . . . . . . . . . . . [445] . . . . . . . . . . .

[446] . . . . . . . . . . . [447] . . . . . . . . . . . [448] . . . . . . . .

. . . [449] . . . . . . . . . . . [450] . .

! 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!

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.