This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex 2016.3.30) 4 APR 2016 17:53 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **uuthesis-2016-guide.ltx (./uuthesis-2016-guide.ltx LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. (/usr/uumath/texlive/2016/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/uumath/texlive/2016/texmf-dist/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 ) (./uuthesis-2016-guide.sty (/usr/uumath/texlive/2016/texmf-dist/tex/latex/tex-gyre/tgbonum.sty Package: tgbonum 2009/09/27 v1.2 TeX Gyre Bonum as default roman family (/usr/uumath/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO) (/usr/uumath/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty Package: keyval 2014/10/28 v1.15 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/uumath/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO) ) (/usr/uumath/texlive/2016/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO) (/usr/uumath/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO) ) (/usr/uumath/texlive/2016/texmf-dist/tex/generic/oberdiek/etexcmds.sty Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO) (/usr/uumath/texlive/2016/texmf-dist/tex/generic/oberdiek/ifluatex.sty Package: ifluatex 2010/03/01 v1.3 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. )))) (/usr/uumath/texlive/2016/texmf-dist/tex/latex/graphics/color.sty Package: color 2016/01/03 v1.1b Standard LaTeX Color (DPC) (/usr/uumath/texlive/2016/texmf-dist/tex/latex/latexconfig/color.cfg File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive ) Package color Info: Driver file: pdftex.def on input line 143. (/usr/uumath/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX \Gread@gobject=\count87 )) (./coloralias.sty Package: coloralias 2004/06/25 v0.00 Support for colorname aliases ) (./rgb.sty Package color Info: Redefining color black on input line 27. Package color Info: Redefining color blue on input line 33. Package color Info: Redefining color cyan on input line 75. Package color Info: Redefining color green on input line 261. Package color Info: Redefining color magenta on input line 457. Package color Info: Redefining color red on input line 559. Package color Info: Redefining color white on input line 654. Package color Info: Redefining color yellow on input line 661. ) Package hocbook Info: Redefining color filecolor on input line 23. ) (./bibnames.sty This is bibnames.sty, Version 1.04 <13 June 1992> (/usr/uumath/texlive/2016/texmf-dist/tex/generic/beebe/texnames.sty This is texnames.sty, Version 1.10 <02 March 1998> )) (./uuthesis-2016-guide.aux) \openout1 = `uuthesis-2016-guide.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 22. LaTeX Font Info: ... okay on input line 22. LaTeX Font Info: Try loading font information for OT1+qbk on input line 22. (/usr/uumath/texlive/2016/texmf-dist/tex/latex/tex-gyre/ot1qbk.fd File: ot1qbk.fd 2009/09/25 v1.2 font definition file for OT1/qbk ) (/usr/uumath/texlive/2016/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count88 \scratchdimen=\dimen103 \scratchbox=\box26 \nofMPsegments=\count89 \nofMParguments=\count90 \everyMPshowfont=\toks15 \MPscratchCnt=\count91 \MPscratchDim=\dimen104 \MPnumerator=\count92 \makeMPintoPDFobject=\count93 \everyMPtoPDFconversion=\toks16 ) LaTeX Font Info: External font `cmex10' loaded for size (Font) <24.88> on input line 26. LaTeX Font Info: External font `cmex10' loaded for size (Font) <20.74> on input line 26. LaTeX Font Info: External font `cmex10' loaded for size (Font) <17.28> on input line 26. LaTeX Font Info: External font `cmex10' loaded for size (Font) <12> on input line 26. LaTeX Font Info: External font `cmex10' loaded for size (Font) <8> on input line 26. LaTeX Font Info: External font `cmex10' loaded for size (Font) <6> on input line 26. (./uuthesis-2016-guide.toc LaTeX Font Info: External font `cmex10' loaded for size (Font) <7> on input line 2. LaTeX Font Info: External font `cmex10' loaded for size (Font) <5> on input line 2. ) \tf@toc=\write3 \openout3 = `uuthesis-2016-guide.toc'. LaTeX Font Info: Try loading font information for OT1+ntxtt on input line 46 . (/usr/uumath/texlive/2016/texmf-dist/tex/latex/newtx/ot1ntxtt.fd File: ot1ntxtt.fd 2012/04/20 v3.1 ) [1 {/usr/uumath/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] LaTeX Font Info: External font `cmex10' loaded for size (Font) <14.4> on input line 103. LaTeX Font Warning: Font shape `OT1/qbk/m/sl' in size <10> not available (Font) Font shape `OT1/qbk/m/it' tried instead on input line 107. [2] LaTeX Font Warning: Font shape `OT1/qbk/m/sl' in size <7> not available (Font) Font shape `OT1/qbk/m/it' tried instead on input line 159. [3] [4] Overfull \hbox (6.74898pt too wide) in paragraph at lines 293--293 []\OT1/ntxtt/m/n/10 \departmentchair {Petrus Marcus Aurelius Featherston e-Hough}[] [] [5] Overfull \hbox (59.24883pt too wide) in paragraph at lines 293--293 []\OT1/ntxtt/m/n/10 \setcounter {page} {2} % UofU demands abstract on p. ii i: start one lower[] [] Overfull \hbox (38.24889pt too wide) in paragraph at lines 293--293 []\OT1/ntxtt/m/n/10 \maintext % Start normal page numbering: parts and ch apters follow.[] [] [6] Overfull \hbox (1.70761pt too wide) in paragraph at lines 340--342 []\OT1/qbk/m/n/10 In both com-mands, col-ors are spec-i-fied by name, and we sh ow shortly [] Overfull \hbox (59.24883pt too wide) in paragraph at lines 367--367 []\OT1/ntxtt/m/n/10 \definecolor{utahheadingcolor} {rgb} {0.700, 0.000, 0.000} % darker Utah red[] [] Overfull \hbox (17.24895pt too wide) in paragraph at lines 367--367 []\OT1/ntxtt/m/n/10 \definecolor{utahtheoremcolor} {rgb} {0.490, 0.149, 0.804} % purple4[] [] [7] LaTeX Font Info: Try loading font information for OMS+qbk on input line 399. LaTeX Font Info: No file OMSqbk.fd. on input line 399. LaTeX Font Warning: Font shape `OMS/qbk/m/n' undefined (Font) using `OMS/cmsy/m/n' instead (Font) for symbol `textbullet' on input line 399. [8] LaTeX Font Warning: Font shape `OT1/qbk/m/sl' in size <9> not available (Font) Font shape `OT1/qbk/m/it' tried instead on input line 481. Overfull \hbox (6.74898pt too wide) in paragraph at lines 513--513 []\OT1/ntxtt/m/n/10 In the figure with green lizards, ... % BAD: where is that figure?[] [] Overfull \hbox (27.74892pt too wide) in paragraph at lines 513--513 []\OT1/ntxtt/m/n/10 In Figure 3, ... % STILL BAD: 3 is a magic number[] [] Overfull \hbox (27.74892pt too wide) in paragraph at lines 513--513 [] \OT1/ntxtt/m/n/10 % that is likely to be wrong the[] [] Overfull \hbox (48.74886pt too wide) in paragraph at lines 513--513 [] \OT1/ntxtt/m/n/10 % next time you upda te the document![] [] Overfull \hbox (22.49893pt too wide) in paragraph at lines 513--513 []\OT1/ntxtt/m/n/10 In Figure \ref{green-lizards}, ... % GOOD: but may be i nconsistent[] [] [9] Overfull \hbox (17.24895pt too wide) in paragraph at lines 513--513 []\OT1/ntxtt/m/n/10 In \figref{green-lizards}, ... % BETTER: uniform no tation and[] [] Overfull \hbox (6.74898pt too wide) in paragraph at lines 513--513 [] \OT1/ntxtt/m/n/10 % label namespace pr otection[] [] Overfull \hbox (22.49893pt too wide) in paragraph at lines 535--535 []\OT1/ntxtt/m/n/10 \newcommand {\figref} [1] {Figure~\ref{fig:#1} \vpager ef{fig:#1}}[] [] Overfull \hbox (17.24895pt too wide) in paragraph at lines 535--535 []\OT1/ntxtt/m/n/10 In \figref{green-lizards}, ... % BETTER: uniform no tation and[] [] Overfull \hbox (6.74898pt too wide) in paragraph at lines 535--535 [] \OT1/ntxtt/m/n/10 % label namespace pr otection[] [] Overfull \hbox (17.24895pt too wide) in paragraph at lines 554--554 []\OT1/ntxtt/m/n/10 \newcommand {\figrefrange} [2] {Figure~\ref{fig:#1} \vpager ef{fig:#1}[] [] Overfull \hbox (22.49893pt too wide) in paragraph at lines 554--554 [] \OT1/ntxtt/m/n/10 Figure~\ref{fig:#2} \vpager ef{fig:#2}}[] [] [10] Overfull \hbox (27.74892pt too wide) in paragraph at lines 643--643 []\OT1/ntxtt/m/n/10 \usepackage {pdfpages} % support for multipage P DF inclusion[] [] Overfull \hbox (32.9989pt too wide) in paragraph at lines 643--643 []\OT1/ntxtt/m/n/10 \usepackage {uuthesis-2016-f} % usual fixups after stan dard packages[] [] [11] Overfull \hbox (22.49893pt too wide) in paragraph at lines 643--643 []\OT1/ntxtt/m/n/10 \usepackage {uuthesis-chapterbib} % support for chapter bib liographies[] [] [12] [13] [14] Overfull \hbox (6.74898pt too wide) in paragraph at lines 872--872 []\OT1/ntxtt/m/n/10 \makeindex % comment out to suppress index ge neration[] [] Overfull \hbox (1.499pt too wide) in paragraph at lines 872--872 []\OT1/ntxtt/m/n/10 \printindex % index is normally last typeset m aterial[] [] [15] [16] Overfull \hbox (1.499pt too wide) in paragraph at lines 944--944 []\OT1/ntxtt/m/n/10 \printindex % index is normally last typeset m aterial[] [] [17] Overfull \hbox (22.49893pt too wide) in paragraph at lines 1050--1050 []\OT1/ntxtt/m/n/10 \newcommand {\bioname} [1] {\emph{\color{blue}#1}\index{#1@ \emph{#1}}}[] [] [18] Overfull \hbox (6.74898pt too wide) in paragraph at lines 1063--1063 []\OT1/ntxtt/m/n/10 \index{sort-key-1@phrase-1!sort-key-2@phrase-2!sort-key-2@p hrase-2}[] [] [19] Overfull \hbox (27.74892pt too wide) in paragraph at lines 1170--1170 []\OT1/ntxtt/m/n/10 grep mainpage thesis.idx | makeindex -c -i thesis.ist > mai n-thesis.ind[] [] [20] Overfull \hbox (1.499pt too wide) in paragraph at lines 1205--1205 []\OT1/ntxtt/m/n/10 egrep -v 'bioname|booktitle|personalname|programname' thesi s.idx |[] [] [21] [22] [23] (./uuthesis-2016-guide.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) Here is how much of TeX's memory you used: 2085 strings out of 493028 30156 string characters out of 6133611 105993 words of memory out of 5000000 5622 multiletter control sequences out of 15000+600000 70044 words of font info for 58 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 44i,8n,23p,321b,318s stack positions out of 5000i,500n,10000p,200000b,80000s {/usr/uumath/texlive/2016/texmf-dist/fonts/enc/dvips/tex-gyre/q-rm.enc}{/usr/ uumath/texlive/2016/texmf-dist/fonts/enc/dvips/tex-gyre/q-rm-sc.enc} Output written on uuthesis-2016-guide.pdf (23 pages, 197040 bytes). PDF statistics: 110 PDF objects out of 1000 (max. 8388607) 77 compressed objects within 1 object stream 0 named destinations out of 1000 (max. 500000) 1 words of extra memory for PDF output out of 10000 (max. 10000000)