pdflatex fails

[dscho]

Even after upgrading the geometry package to a newer version, upgrading Ubuntu to 13.10, compiling LyX manually, the compilation fails:

  Mon Feb 17 16:56:40 UTC 2014, Creating IJ 1.46r guide:

  -->  Detecting pdflatex...
  -->  Running LyX2TeX. Please wait...
grep: /usr/share/texmf-texlive/tex/latex/geometry/geometry.sty: No such file or directory
  -->  2s. Cleaning lyx directory...
  -->  Moving converted files to tex directory...
  -->  Compiling main PDF. Please wait...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
 restricted \write18 enabled.
entering extended mode
(./user-guide.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin9.def))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))

Package Babel Warning: The package option `english' should not be used
(Babel)                with a more specific one (like `american') on input line
 14.

(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/varioref.sty)
(/usr/share/texlive/texmf-dist/tex/latex/prettyref/prettyref.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/units/units.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/units/nicefrac.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdfpages/pdfpages.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/eso-pic/eso-pic.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/atbegshi.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/pdfpages/pppdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file user-guide.idx
(/usr/share/texlive/texmf-dist/tex/latex/setspace/setspace.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty)
(/usr/share/texlive/texmf-dist/tex/latex/nomencl/nomencl.sty)
Writing nomenclature file user-guide.nlo
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 47.

! Package float Error: Unknown float style `' .

See the float package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.81 \floatstyle{}

(/usr/share/texlive/texmf-dist/tex/latex/tocloft/tocloft.sty

! LaTeX Error: Missing \begin{document}.

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

l.64 \ProcessOptions\relax

! Missing { inserted.
<to be read again> 
                   \let 
l.64 \ProcessOptions\relax

)
Runaway text?
\let \ds@titles \@empty \fi \fi \@iforloop subfigure,\@nil ,\@nil \@@ \ETC.
! File ended while scanning text of \toks@.
<inserted text> 
                }
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper alphabetic constant.
<to be read again> 
                   \spacefactor 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Invalid code (1000), should be in the range 0..15.
<recently read> \spacefactor 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Missing $ inserted.
<inserted text> 
                $
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
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                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   let 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   =
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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<to be read again> 
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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   edef 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Improper `at' size (0.0pt), replaced by 10pt.
<recently read> @tempdimb 

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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
                   <
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Missing number, treated as zero.
<to be read again> 
                   def 
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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
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                   def 
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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   def 
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                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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                   def 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Missing number, treated as zero.
<to be read again> 
                   def 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
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                   def 
l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...

! Illegal unit of measure (pt inserted).
<to be read again> 
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l.101 \addtolength
                  {\cftsubsecnumwidth}{6pt} % make space for more than 10 su...
(That makes 100 errors; please try again.)
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on user-guide.log.

Any insight?

[tferr]

Not so sure what is going on. We seem to be using the same TeX distribution.

You mention having to update geometry: Could you please update the package cache by running texhash (on my installation I have to use sudo texhash). I always though tlmgr would do it, but perhaps I've been wrong?

Another shot in dark: If I got it right, a diff between my output and yours seems to indicate that some packages were not loaded. Could you please check if you have all of these installed?

/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
/usr/share/texlive/texmf-dist/tex/latex/mparhack/mparhack.sty
/usr/share/texlive/texmf-dist/tex/latex/microtype/microtype.sty
/usr/share/texlive/texmf-dist/tex/latex/microtype/microtype-pdftex.def
/usr/share/texlive/texmf-dist/tex/latex/microtype/microtype.cfg
/usr/share/texlive/texmf-dist/tex/latex/sectsty/sectsty.sty
/usr/share/texlive/texmf-dist/tex/latex/appendix/appendix.sty
/usr/share/texlive/texmf-dist/tex/latex/SIunits/SIunits.sty

[dscho]

The output I pasted was from a fully up-to-date texlive-latex-extra installation on Ubuntu 13.10 without any local hacks. Same for lyx.

The comments you saw about updating geometry and lyx locally stemmed from some experiments with Ubuntu 12.04 (a Long Term Support version) because my original plan was to let Jenkins build & serve your guide (and I cannot flimiscally update the server to a non-LTS version or mess with the installed packages as if I had a single user machine).

[dscho]

FWIW I also hoped that I could patch the guide to make it possible to compile with more easily installed setups, to attract more contributors, but I fail even to compile the guide myself as it stands now...

[tferr]

Wow, that would be great. Really really appreciated. Thanks for that!

Please bear with my lack of analytical skills to solve this issue. I really did not know where to start. Now that I know you are using texlive-latex-extra, I just looked at the list of CTAN packages included in it, and it seems that at least microtype, and SIunits are not included. That could be sufficient to stop the file from compiling (I'm guessing here).

I am using 'vanilla' MacTeX, and only now I am realizing that the debian distribution of TeX live 2013 may be different. Also, only now I realized that in Ubuntu, tlmgr is not available from the repositories and can only be installed manually (do you confirm this?).

Here is what I will try to do: I will try to remove the requirements for the packages not listed in the Debian texlive-extra list. If I fail, i.e., if some packages at CTAN that are not included in texlive-latex-extra are really required (I went through this exercise of using only as little requirements as possible back in 2012), could we included download links for them in the building script, or is that a bad practice?

Meanwhile, I would ask you a favor: with tlmgr, we could run tlmgr list --only-installed to obtain a list of all the packages installed. Without it, could you please send me all the list of files in /texlive/texmf-dist/tex/latex/ that got installed in your system? (sorry to ask you this, but I only have access to my laptop and I'm afraid I may get a wrong list if I try elsewhere).

Also, please know I am really surprised that there are different TeX live distributions. I guess I do not understand the concept of a live distribution then.

[tferr]

Forgot to include this link to tex.stackexchange, in case it helps. Here, it seems that it is possible to obtain a list of all the installed LaTeX packages in Ubuntu using kpsepath as an alternative to tlmgr

Also, It seems that others also had the need to have access to all the CTAN repertoire of LaTeX packages, rather then relying on the ones pre-selected by apt-get. Would this help us https://github.com/scottkosty/install-tl-ubuntu#install-tl-ubuntu ?

[tferr]

OK, just had a look at all the CTAN packages required (see https://github.com/tferr/IJ-guide/commit/4b5dc762e2d2ed52764ebf4fb28b8bee833cc5da) and looked more carefully into this. I can obtain your error when I remove IJguide.module from the lyx layouts folder. IJguide.module is a common LaTeX preamble that gets applied to all the tex files (the README should describe this).

When I remove IJguide.module from the lyx user directory I get lots of "Warning: Module not available" messages when running lyx --force-overwrite --export pdflatex user-guide.lyx. Did you get this type of messages?

If IJguide.module is not symlinked in your lyx layout folder: The lyx layout folder is in the lyx user directory. If can be created if it does not exist. Unfortunately, I don't know how to check its path from the command line. I only know how to get its path using the LyX GUI, by clicking in LyX>About. In Ubuntu it looks as if it could be ~/.lyx/layouts or /usr/share/lyx/layouts. Once IJguide.module is symlinked there, lyx needs to be reconfigured. I think this can be done using lyx --execute reconfigure

If this is indeed the issue: Lyx seems to have a command line option to set the user directory, so I guess this could be improved

[tferr]

@dscho sorry for the delay. I think I got it, but had to install lubuntu 13.10 (through VirtualBox) to really see what was going on. This was really a fresh out-of-the-box lubuntu install. I came across two major problems:

1. sudo apt-get install lyx did install a capable texlive, but it did not seem to install scalable fonts. So I removed the requirements for it. https://github.com/tferr/IJ-guide/commit/d70925e804ed6d79c79fb7eec1bf783e865663d6 should have solved this.
2. The other problem was that lyx was not aware of IJguide.module. This made me realize that the kludgy compile script was extremely mac-centric, so it was renamed to compileMac.sh with https://github.com/tferr/IJ-guide/commit/6ef08986fccc96a73d0e71513f2da0bf0eec3fb9

With https://github.com/tferr/IJ-guide/commit/f261d2cd80da2f380d1551baf498595a2067d74d CompileLinux.sh was added that successfully built the 3 pdfs.

Could you please give it a try?