The document now compiles without error using TeXLive2021 (and the 2020 version of texlive-extra), but the bibliography still does not print in the PDF.
The latex.log has these warnings: LaTeX Warning: Citation 'Groot1991' on page 4 undefined on input line 151. LaTeX Warning: Citation 'Marcoe2018' on page 4 undefined on input line 167. Lines 149-151 in the .lyx file are: \begin_layout Standard \begin_inset ERT status open and lines 163-167 are: \begin_inset CommandInset toc LatexCommand tableofcontents \end_inset There are other warnings at the top of the (attached) latex.log file and I need help understanding what the warnings mean. TIA, Rich
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021 on Slint) (preloaded format=pdflatex 2021.10.13) 13 OCT 2021 15:36 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **biological-evaluation.tex (./biological-evaluation.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-02-18> (/usr/share/texmf-dist/tex/latex/koma-script/scrreprt.cls Document Class: scrreprt 2021/03/17 v3.33 KOMA-Script document class (report) (/usr/share/texmf-dist/tex/latex/koma-script/scrkbase.sty Package: scrkbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-dependent b asics and keyval usage) (/usr/share/texmf-dist/tex/latex/koma-script/scrbase.sty Package: scrbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-independent basics and keyval usage) (/usr/share/texmf-dist/tex/latex/koma-script/scrlfile.sty Package: scrlfile 2021/03/17 v3.33 KOMA-Script package (file load hooks) (/usr/share/texmf-dist/tex/latex/koma-script/scrlfile-hook.sty Package: scrlfile-hook 2021/03/17 v3.33 KOMA-Script package (using LaTeX hooks) LaTeX3 Info: Defining command \BeforeFile with sig. 'm' on line 61. LaTeX3 Info: Defining command \AfterFile with sig. 'm' on line 65. LaTeX3 Info: Defining command \BeforeClass with sig. 'm' on line 69. LaTeX3 Info: Defining command \BeforePackage with sig. 'm' on line 73. LaTeX3 Info: Defining command \AfterAtEndOfClass with sig. 'smo+m' on line 83. LaTeX3 Info: Defining command \AfterAtEndOfPackage with sig. 'smo+m' on line (LaTeX3) 93. LaTeX3 Info: Defining command \scrlfile@AfterClass with sig. 'smo+m' on line (LaTeX3) 173. LaTeX3 Info: Defining command \AfterClass with sig. '' on line 174. LaTeX3 Info: Defining command \scrlfile@AfterPackage with sig. 'smo+m' on line (LaTeX3) 191. LaTeX3 Info: Defining command \AfterPackage with sig. '' on line 192. LaTeX3 Info: Defining command \ReplaceInput with sig. '' on line 193. LaTeX3 Info: Defining command \ReplaceClass with sig. 'mm' on line 196. LaTeX3 Info: Defining command \ReplacePackage with sig. 'mm' on line 199. LaTeX3 Info: Defining command \UnReplaceInput with sig. '' on line 200. LaTeX3 Info: Defining command \UnReplaceClass with sig. 'm' on line 203. LaTeX3 Info: Defining command \UnReplacePackage with sig. 'mm' on line 206. LaTeX3 Info: Defining command \PreventPackageFromLoading with sig. 's+om' on (LaTeX3) line 234. LaTeX3 Info: Defining command \StorePreventPackageFromLoading with sig. 'm' on (LaTeX3) line 242. LaTeX3 Info: Defining command \ResetPreventPackageFromLoading with sig. '' on (LaTeX3) line 247. LaTeX3 Info: Defining command \UnPreventPackageFromLoading with sig. 'sm' on (LaTeX3) line 261. LaTeX3 Info: Defining command \BeforeClosingMainAux with sig. 'om' on line (LaTeX3) 274. LaTeX3 Info: Defining command \AfterReadingMainAux with sig. 'om' on line 287. LaTeX3 Info: Defining command \protected@immediate@write with sig. 'm+m+m' on (LaTeX3) line 298. (/usr/share/texmf-dist/tex/latex/koma-script/scrlogo.sty Package: scrlogo 2021/03/17 v3.33 KOMA-Script package (logo) ))) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty Package: keyval 2014/10/28 v1.15 key=value parser (DPC) \KV@toks@=\toks15 ) Skipping: [2021/05/01] Usage of raw option list on input line 252. Applying: [0000/00/00] compatibility for LaTeX before 2021/05/01 on input line 337. )) (/usr/share/texmf-dist/tex/latex/koma-script/tocbasic.sty Package: tocbasic 2021/03/17 v3.33 KOMA-Script package (handling toc-files) \scr@dte@tocline@numberwidth=\skip47 \scr@dte@tocline@numbox=\box47 ) Package tocbasic Info: babel extension for `toc' omitted (tocbasic) because of missing \bbl@set@language on input line 137. Class scrreprt Info: File `scrsize11pt.clo' used instead of (scrreprt) file `scrsize11.clo' to setup font sizes on input line 245 1. (/usr/share/texmf-dist/tex/latex/koma-script/scrsize11pt.clo File: scrsize11pt.clo 2021/03/17 v3.33 KOMA-Script font size class option (11pt ) ) (/usr/share/texmf-dist/tex/latex/koma-script/typearea.sty Package: typearea 2021/03/17 v3.33 KOMA-Script package (type area) \ta@bcor=\skip48 \ta@div=\count179 \ta@hblk=\skip49 \ta@vblk=\skip50 \ta@temp=\skip51 \footheight=\skip52 Package typearea Info: These are the values describing the layout: (typearea) DIV = 10 (typearea) BCOR = 0.0pt (typearea) \paperwidth = 597.50793pt (typearea) \textwidth = 418.25555pt (typearea) DIV departure = -6% (typearea) \evensidemargin = 47.2316pt (typearea) \oddsidemargin = -12.5192pt (typearea) \paperheight = 845.04694pt (typearea) \textheight = 514.20023pt (typearea) \topmargin = 12.2347pt (typearea) \headheight = 17.0pt (typearea) \headsep = 20.40001pt (typearea) \topskip = 11.0pt (typearea) \footskip = 47.6pt (typearea) \baselineskip = 13.6pt (typearea) on input line 1741. ) \c@part=\count180 \c@chapter=\count181 \c@section=\count182 \c@subsection=\count183 \c@subsubsection=\count184 \c@paragraph=\count185 \c@subparagraph=\count186 \scr@dte@chapter@maxnumwidth=\skip53 Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\chapter on input line 5678. \scr@dte@section@maxnumwidth=\skip54 Class scrreprt Info: using compatibility default `runin=bysign' (scrreprt) for `\section on input line 5689. Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\section on input line 5689. \scr@dte@part@maxnumwidth=\skip55 Class scrreprt Info: using compatibility default `afterindent=true' (scrreprt) for `\part on input line 5698. \scr@dte@subsection@maxnumwidth=\skip56 Class scrreprt Info: using compatibility default `runin=bysign' (scrreprt) for `\subsection on input line 5708. Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\subsection on input line 5708. \scr@dte@subsubsection@maxnumwidth=\skip57 Class scrreprt Info: using compatibility default `runin=bysign' (scrreprt) for `\subsubsection on input line 5718. Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\subsubsection on input line 5718. \scr@dte@paragraph@maxnumwidth=\skip58 Class scrreprt Info: using compatibility default `runin=bysign' (scrreprt) for `\paragraph on input line 5729. Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\paragraph on input line 5729. \scr@dte@subparagraph@maxnumwidth=\skip59 Class scrreprt Info: using compatibility default `runin=bysign' (scrreprt) for `\subparagraph on input line 5739. Class scrreprt Info: using compatibility default `afterindent=bysign' (scrreprt) for `\subparagraph on input line 5739. \abovecaptionskip=\skip60 \belowcaptionskip=\skip61 \c@pti@nb@sid@b@x=\box48 Package tocbasic Info: babel extension for `lof' omitted (tocbasic) because of missing \bbl@set@language on input line 6976. \scr@dte@figure@maxnumwidth=\skip62 \c@figure=\count187 Package tocbasic Info: babel extension for `lot' omitted (tocbasic) because of missing \bbl@set@language on input line 6993. \scr@dte@table@maxnumwidth=\skip63 \c@table=\count188 Class scrreprt Info: Redefining `\numberline' on input line 7162. \bibindent=\dimen138 ) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty Package: fontenc 2020/08/10 v2.0s Standard LaTeX package ) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty Package: inputenc 2020/08/01 v1.3d Input encoding file \inpenc@prehook=\toks16 \inpenc@posthook=\toks17 (/usr/share/texmf-dist/tex/latex/base/latin9.def File: latin9.def 2020/08/01 v1.3d Input encoding file )) (/usr/share/texmf-dist/tex/latex/geometry/geometry.sty Package: geometry 2020/01/02 v5.9 Page Geometry (/usr/share/texmf-dist/tex/generic/iftex/ifvtex.sty Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead. (/usr/share/texmf-dist/tex/generic/iftex/iftex.sty Package: iftex 2020/03/06 v1.0d TeX engine tests )) \Gm@cnth=\count189 \Gm@cntv=\count190 \c@Gm@tempcnt=\count191 \Gm@bindingoffset=\dimen139 \Gm@wd@mp=\dimen140 \Gm@odd@mp=\dimen141 \Gm@even@mp=\dimen142 \Gm@layoutwidth=\dimen143 \Gm@layoutheight=\dimen144 \Gm@layouthoffset=\dimen145 \Gm@layoutvoffset=\dimen146 \Gm@dimlist=\toks18 ) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty Package: textcomp 2020/02/02 v2.0n Standard LaTeX package ) (/usr/share/texmf-dist/tex/latex/url/url.sty \Urlmuskip=\muskip16 Package: url 2013/09/16 ver 3.4 Verb mode for urls, etc. ) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty Package: graphicx 2020/09/09 v1.2b Enhanced LaTeX Graphics (DPC,SPQR) (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty Package: graphics 2020/08/30 v1.4c Standard LaTeX Graphics (DPC,SPQR) (/usr/share/texmf-dist/tex/latex/graphics/trig.sty Package: trig 2016/01/03 v1.10 sin cos tan (DPC) ) (/usr/share/texmf-dist/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. (/usr/share/texmf-dist/tex/latex/graphics-def/pdftex.def File: pdftex.def 2020/10/05 v1.2a Graphics/color driver for pdftex )) \Gin@req@height=\dimen147 \Gin@req@width=\dimen148 ) (/usr/share/texmf-dist/tex/latex/psnfss/mathpazo.sty Package: mathpazo 2020/03/25 PSNFSS-v9.3 Palatino w/ Pazo Math (D.Puga, WaS) \symupright=\mathgroup4 ) (/usr/share/texmf-dist/tex/latex/relsize/relsize.sty Package: relsize 2013/03/29 ver 4.1 ) (/usr/share/texmf-dist/tex/latex/koma-script/scrlayer-scrpage.sty Package: scrlayer-scrpage 2021/03/17 v3.33 KOMA-Script package (end user interf ace for scrlayer) (/usr/share/texmf-dist/tex/latex/koma-script/scrlayer.sty Package: scrlayer 2021/03/17 v3.33 KOMA-Script package (defining layers and pag e styles) Package scrlayer Info: Using already defined \footheight (scrlayer) hoping, that this is a length and (scrlayer) not only a macro on input line 136. Package scrlayer Info: patching LaTeX kernel macro \pagestyle on input line 216 2. ) Package scrlayer-scrpage Info: Makeing stand-alone element `pagehead' from (scrlayer-scrpage) alias to `pageheadfoot' on input line 1085. Package scrlayer-scrpage Info: deactivating warning for font element (scrlayer-scrpage) `pagefoot' on input line 1109. ) Package scrlayer-scrpage Info: auto-selection of `pagestyleset=KOMA-Script'. 1: section (/usr/share/texmf-dist/tex/latex/biblatex/biblatex.sty Package: biblatex 2019/12/01 v3.14 programmable bibliographies (PK/MW) (/usr/share/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty Package: pdftexcmds 2020-06-27 v0.33 Utility functions of pdfTeX for LuaTeX (HO ) (/usr/share/texmf-dist/tex/generic/infwarerr/infwarerr.sty Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO) ) (/usr/share/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty Package: ltxcmds 2020-05-10 v1.25 LaTeX kernel commands for general use (HO) ) Package pdftexcmds Info: \pdf@primitive is available. Package pdftexcmds Info: \pdf@ifprimitive is available. Package pdftexcmds Info: \pdfdraftmode found. ) (/usr/share/texmf-dist/tex/latex/etoolbox/etoolbox.sty Package: etoolbox 2020/10/05 v2.5k e-TeX tools for LaTeX (JAW) \etb@tempcnta=\count192 ) (/usr/share/texmf-dist/tex/latex/kvoptions/kvoptions.sty Package: kvoptions 2020-10-07 v3.14 Key value format for package options (HO) (/usr/share/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty Package: kvsetkeys 2019/12/15 v1.18 Key value parser (HO) )) (/usr/share/texmf-dist/tex/latex/logreq/logreq.sty Package: logreq 2010/08/04 v1.0 xml request logger \lrq@indent=\count193 (/usr/share/texmf-dist/tex/latex/logreq/logreq.def File: logreq.def 2010/08/04 v1.0 logreq spec v1.0 )) (/usr/share/texmf-dist/tex/latex/base/ifthen.sty Package: ifthen 2014/09/29 v1.1c Standard LaTeX ifthen package (DPC) ) \c@tabx@nest=\count194 \c@listtotal=\count195 \c@listcount=\count196 \c@liststart=\count197 \c@liststop=\count198 \c@citecount=\count199 \c@citetotal=\count266 \c@multicitecount=\count267 \c@multicitetotal=\count268 \c@instcount=\count269 \c@maxnames=\count270 \c@minnames=\count271 \c@maxitems=\count272 \c@minitems=\count273 \c@citecounter=\count274 \c@maxcitecounter=\count275 \c@savedcitecounter=\count276 \c@uniquelist=\count277 \c@uniquename=\count278 \c@refsection=\count279 \c@refsegment=\count280 \c@maxextratitle=\count281 \c@maxextratitleyear=\count282 \c@maxextraname=\count283 \c@maxextradate=\count284 \c@maxextraalpha=\count285 \c@abbrvpenalty=\count286 \c@highnamepenalty=\count287 \c@lownamepenalty=\count288 \c@maxparens=\count289 \c@parenlevel=\count290 \blx@tempcnta=\count291 \blx@tempcntb=\count292 \blx@tempcntc=\count293 \blx@maxsection=\count294 \blx@maxsegment@0=\count295 \blx@notetype=\count296 \blx@parenlevel@text=\count297 \blx@parenlevel@foot=\count298 \blx@sectionciteorder@0=\count299 \blx@entrysetcounter=\count300 \labelnumberwidth=\skip64 \labelalphawidth=\skip65 \biblabelsep=\skip66 \bibitemsep=\skip67 \bibnamesep=\skip68 \bibinitsep=\skip69 \bibparsep=\skip70 \bibhang=\skip71 \blx@bcfin=\read2 \blx@bcfout=\write3 \blx@langwohyphens=\language87 \c@mincomprange=\count301 \c@maxcomprange=\count302 \c@mincompwidth=\count303 Package biblatex Info: Trying to load biblatex default data model... Package biblatex Info: ... file 'blx-dm.def' found. (/usr/share/texmf-dist/tex/latex/biblatex/blx-dm.def File: blx-dm.def 2019/12/01 v3.14 biblatex localization (PK/MW) ) Package biblatex Info: Trying to load biblatex style data model... Package biblatex Info: ... file 'authoryear.dbx' not found. Package biblatex Info: Trying to load biblatex custom data model... Package biblatex Info: ... file 'biblatex-dm.cfg' not found. \c@afterword=\count304 \c@savedafterword=\count305 \c@annotator=\count306 \c@savedannotator=\count307 \c@author=\count308 \c@savedauthor=\count309 \c@bookauthor=\count310 \c@savedbookauthor=\count311 \c@commentator=\count312 \c@savedcommentator=\count313 \c@editor=\count314 \c@savededitor=\count315 \c@editora=\count316 \c@savededitora=\count317 \c@editorb=\count318 \c@savededitorb=\count319 \c@editorc=\count320 \c@savededitorc=\count321 \c@foreword=\count322 \c@savedforeword=\count323 \c@holder=\count324 \c@savedholder=\count325 \c@introduction=\count326 \c@savedintroduction=\count327 \c@namea=\count328 \c@savednamea=\count329 \c@nameb=\count330 \c@savednameb=\count331 \c@namec=\count332 \c@savednamec=\count333 \c@translator=\count334 \c@savedtranslator=\count335 \c@shortauthor=\count336 \c@savedshortauthor=\count337 \c@shorteditor=\count338 \c@savedshorteditor=\count339 \c@labelname=\count340 \c@savedlabelname=\count341 \c@institution=\count342 \c@savedinstitution=\count343 \c@lista=\count344 \c@savedlista=\count345 \c@listb=\count346 \c@savedlistb=\count347 \c@listc=\count348 \c@savedlistc=\count349 \c@listd=\count350 \c@savedlistd=\count351 \c@liste=\count352 \c@savedliste=\count353 \c@listf=\count354 \c@savedlistf=\count355 \c@location=\count356 \c@savedlocation=\count357 \c@organization=\count358 \c@savedorganization=\count359 \c@origlocation=\count360 \c@savedoriglocation=\count361 \c@origpublisher=\count362 \c@savedorigpublisher=\count363 \c@publisher=\count364 \c@savedpublisher=\count365 \c@language=\count366 \c@savedlanguage=\count367 \c@origlanguage=\count368 \c@savedoriglanguage=\count369 \c@pageref=\count370 \c@savedpageref=\count371 \shorthandwidth=\skip72 \shortjournalwidth=\skip73 \shortserieswidth=\skip74 \shorttitlewidth=\skip75 \shortauthorwidth=\skip76 \shorteditorwidth=\skip77 \locallabelnumberwidth=\skip78 \locallabelalphawidth=\skip79 \localshorthandwidth=\skip80 \localshortjournalwidth=\skip81 \localshortserieswidth=\skip82 \localshorttitlewidth=\skip83 \localshortauthorwidth=\skip84 \localshorteditorwidth=\skip85 Package biblatex Info: Trying to load compatibility code... Package biblatex Info: ... file 'blx-compat.def' found. (/usr/share/texmf-dist/tex/latex/biblatex/blx-compat.def File: blx-compat.def 2019/12/01 v3.14 biblatex compatibility (PK/MW) ) Package biblatex Info: Trying to load generic definitions... Package biblatex Info: ... file 'biblatex.def' found. (/usr/share/texmf-dist/tex/latex/biblatex/biblatex.def File: biblatex.def 2019/12/01 v3.14 biblatex compatibility (PK/MW) \c@textcitecount=\count372 \c@textcitetotal=\count373 \c@textcitemaxnames=\count374 \c@biburlbigbreakpenalty=\count375 \c@biburlbreakpenalty=\count376 \c@biburlnumpenalty=\count377 \c@biburlucpenalty=\count378 \c@biburllcpenalty=\count379 \biburlbigskip=\muskip17 \biburlnumskip=\muskip18 \biburlucskip=\muskip19 \biburllcskip=\muskip20 \c@smartand=\count380 ) Package biblatex Info: Trying to load natbib compatibility... Package biblatex Info: ... file 'blx-natbib.def' found. (/usr/share/texmf-dist/tex/latex/biblatex/blx-natbib.def File: blx-natbib.def 2019/12/01 v3.14 biblatex compatibility (PK/MW) Package biblatex Info: Delimiter 'nameyeardelim' in context '' already defined, overwriting. ) Package biblatex Info: Trying to load bibliography style 'authoryear'... Package biblatex Info: ... file 'authoryear.bbx' found. (/usr/share/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx File: authoryear.bbx 2019/12/01 v3.14 biblatex bibliography style (PK/MW) Package biblatex Info: Trying to load bibliography style 'standard'... Package biblatex Info: ... file 'standard.bbx' found. (/usr/share/texmf-dist/tex/latex/biblatex/bbx/standard.bbx File: standard.bbx 2019/12/01 v3.14 biblatex bibliography style (PK/MW) \c@bbx:relatedcount=\count381 \c@bbx:relatedtotal=\count382 )) Package biblatex Info: Trying to load citation style 'authoryear'... Package biblatex Info: ... file 'authoryear.cbx' found. (/usr/share/texmf-dist/tex/latex/biblatex/cbx/authoryear.cbx File: authoryear.cbx 2019/12/01 v3.14 biblatex citation style (PK/MW) Package biblatex Info: Redefining '\cite'. Package biblatex Info: Redefining '\parencite'. Package biblatex Info: Redefining '\footcite'. Package biblatex Info: Redefining '\footcitetext'. Package biblatex Info: Redefining '\smartcite'. Package biblatex Info: Redefining '\textcite'. Package biblatex Info: Redefining '\textcites'. ) Package biblatex Info: Trying to load configuration file... Package biblatex Info: ... file 'biblatex.cfg' found. (/usr/share/texmf-dist/tex/latex/biblatex/biblatex.cfg File: biblatex.cfg )) \@quotelevel=\count383 \@quotereset=\count384 LaTeX Font Info: Trying to load font information for T1+ppl on input line 45 . (/usr/share/texmf-dist/tex/latex/psnfss/t1ppl.fd File: t1ppl.fd 2001/06/04 font definitions for T1/ppl. ) (/usr/share/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def File: l3backend-pdftex.def 2021-03-18 L3 backend support: PDF output (pdfTeX) \l__color_backend_stack_int=\count385 \l__pdf_internal_box=\box49 ) (./biological-evaluation.aux) \openout1 = `biological-evaluation.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 45. LaTeX Font Info: ... okay on input line 45. Package scrbase Info: activating english \contentsname on input line 45. Package scrbase Info: activating english \listfigurename on input line 45. Package scrbase Info: activating english \listtablename on input line 45. *geometry* driver: auto-detecting *geometry* detected driver: pdftex Package geometry Warning: The marginal notes overrun the paper. Add 28.75017pt and more to the right margin. *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: letterpaper * layout: <same size as paper> * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: twoside * h-part:(L,W,R)=(56.9055pt, 483.67337pt, 73.71613pt) * v-part:(T,H,B)=(113.81102pt, 624.25346pt, 56.9055pt) * \paperwidth=614.295pt * \paperheight=794.96999pt * \textwidth=483.67337pt * \textheight=624.25346pt * \oddsidemargin=-15.36449pt * \evensidemargin=1.44614pt * \topmargin=-18.13809pt * \headheight=17.0pt * \headsep=42.67912pt * \topskip=11.0pt * \footskip=47.6pt * \marginparwidth=89.62619pt * \marginparsep=12.8401pt * \columnsep=10.0pt * \skip\footins=10.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidetrue * \@mparswitchtrue * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count386 \scratchdimen=\dimen149 \scratchbox=\box50 \nofMPsegments=\count387 \nofMParguments=\count388 \everyMPshowfont=\toks19 \MPscratchCnt=\count389 \MPscratchDim=\dimen150 \MPnumerator=\count390 \makeMPintoPDFobject=\count391 \everyMPtoPDFconversion=\toks20 ) (/usr/share/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf (/usr/share/texmf-dist/tex/latex/grfext/grfext.sty Package: grfext 2019/12/03 v1.3 Manage graphics extensions (HO) (/usr/share/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO) )) Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4 85. 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 504. (/usr/share/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv e )) \big@size=\dimen151 Package biblatex Info: Trying to load language 'english'... Package biblatex Info: ... file 'english.lbx' found. (/usr/share/texmf-dist/tex/latex/biblatex/lbx/english.lbx File: english.lbx 2019/12/01 v3.14 biblatex localization (PK/MW) ) Package biblatex Info: Input encoding 'latin9' detected. Package biblatex Info: Automatic encoding selection. (biblatex) Assuming data encoding 'latin9'. \openout3 = `biological-evaluation.bcf'. Package biblatex Info: Trying to load bibliographic data... Package biblatex Info: ... file 'biological-evaluation.bbl' not found. No file biological-evaluation.bbl. Package biblatex Info: Reference section=0 on input line 45. Package biblatex Info: Reference segment=0 on input line 45. <1_home_rshepard_documents_templates_llc-letterhead.pdf, id=1, 530.02815pt x 15 7.62086pt> File: 1_home_rshepard_documents_templates_llc-letterhead.pdf Graphic file (type pdf) <use 1_home_rshepard_documents_templates_llc-letterhead.pdf> Package pdftex.def Info: 1_home_rshepard_documents_templates_llc-letterhead.pdf used on input line 56. (pdftex.def) Requested size: 483.67337pt x 143.84166pt. LaTeX Font Info: Trying to load font information for T1+cmss on input line 5 6. (/usr/share/texmf-dist/tex/latex/base/t1cmss.fd File: t1cmss.fd 2019/12/16 v2.5j Standard LaTeX font definitions ) LaTeX Font Info: Trying to load font information for OT1+ppl on input line 5 6. (/usr/share/texmf-dist/tex/latex/psnfss/ot1ppl.fd File: ot1ppl.fd 2001/06/04 font definitions for OT1/ppl. ) LaTeX Font Info: Trying to load font information for OML+zplm on input line 56. (/usr/share/texmf-dist/tex/latex/psnfss/omlzplm.fd File: omlzplm.fd 2002/09/08 Fontinst v1.914 font definitions for OML/zplm. ) LaTeX Font Info: Trying to load font information for OMS+zplm on input line 56. (/usr/share/texmf-dist/tex/latex/psnfss/omszplm.fd File: omszplm.fd 2002/09/08 Fontinst v1.914 font definitions for OMS/zplm. ) LaTeX Font Info: Trying to load font information for OMX+zplm on input line 56. (/usr/share/texmf-dist/tex/latex/psnfss/omxzplm.fd File: omxzplm.fd 2002/09/08 Fontinst v1.914 font definitions for OMX/zplm. ) LaTeX Font Info: Trying to load font information for OT1+zplm on input line 56. (/usr/share/texmf-dist/tex/latex/psnfss/ot1zplm.fd File: ot1zplm.fd 2002/09/08 Fontinst v1.914 font definitions for OT1/zplm. ) LaTeX Warning: No \author given. [1 {/usr/share/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./1_home_rshepard_do cuments_templates_llc-letterhead.pdf>] (./biological-evaluation.toc) \tf@toc=\write4 \openout4 = `biological-evaluation.toc'. [1 ] (./biological-evaluation.lof Overfull \hbox (3.70705pt too wide) in paragraph at lines 11--11 \T1/ppl/m/n/10.95 River, Ore-gon.". Pub-lished by West-ern Color Sales Inc., P ort-land, Ore-gon. Card #K1806. [] ) \tf@lof=\write5 \openout5 = `biological-evaluation.lof'. [2 ] chapter 1. <2_home_rshepard_projects_washington_nevins-dock_images_nevins-project.png, id= 28, 908.39375pt x 875.27pt> File: 2_home_rshepard_projects_washington_nevins-dock_images_nevins-project.png Graphic file (type png) <use 2_home_rshepard_projects_washington_nevins-dock_images_nevins-project.png> Package pdftex.def Info: 2_home_rshepard_projects_washington_nevins-dock_images _nevins-project.png used on input line 95. (pdftex.def) Requested size: 483.67337pt x 466.04112pt. <3_home_rshepard_projects_washington_nevins-dock_images_bathymetry.png, id=30, 803.0pt x 602.25pt> File: 3_home_rshepard_projects_washington_nevins-dock_images_bathymetry.png Gra phic file (type png) <use 3_home_rshepard_projects_washington_nevins-dock_images_bathymetry.png> Package pdftex.def Info: 3_home_rshepard_projects_washington_nevins-dock_images _bathymetry.png used on input line 113. (pdftex.def) Requested size: 483.67337pt x 287.19133pt. [1 ] [2 <./2_home_rshepard_projects_washington_nevins-dock_images_nevins-project.p ng (PNG copy)>] [3 <./3_home_rshepard_projects_washington_nevins-dock_images_ba thymetry.png>] chapter 2. LaTeX Warning: Citation 'Groot1991' on page 4 undefined on input line 151. LaTeX Warning: Citation 'Marcoe2018' on page 4 undefined on input line 167. LaTeX Font Info: Trying to load font information for T1+cmtt on input line 1 79. (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd File: t1cmtt.fd 2019/12/16 v2.5j Standard LaTeX font definitions ) [4 ] LaTeX Font Info: Trying to load font information for TS1+ppl on input line 1 90. (/usr/share/texmf-dist/tex/latex/psnfss/ts1ppl.fd File: ts1ppl.fd 2001/06/04 font definitions for TS1/ppl. ) [5] <4_home_rshepard_projects_washington_nevins-dock_images_sandy_river_smelting.jp g, id=57, 96.36pt x 61.9113pt> File: 4_home_rshepard_projects_washington_nevins-dock_images_sandy_river_smelti ng.jpg Graphic file (type jpg) <use 4_home_rshepard_projects_washington_nevins-dock_images_sandy_river_smeltin g.jpg> Package pdftex.def Info: 4_home_rshepard_projects_washington_nevins-dock_images _sandy_river_smelting.jpg used on input line 278. (pdftex.def) Requested size: 483.67337pt x 310.81114pt. [6] [7 <./4_home_rshepard_projects_washington_nevins-dock_images_sandy_river_sm elting.jpg>] LaTeX Warning: Citation 'VanDoornik2019' on page 8 undefined on input line 356. [8] LaTeX Warning: Citation 'Keefer2008' on page 9 undefined on input line 365. LaTeX Warning: Citation 'Johnson2005' on page 9 undefined on input line 390. [9] LaTeX Warning: Citation 'McCabe1994' on page 10 undefined on input line 429. [10] chapter 3. <5_home_rshepard_projects_washington_nevins-dock_analyses_current.pdf, id=76, 4 33.62pt x 433.62pt> File: 5_home_rshepard_projects_washington_nevins-dock_analyses_current.pdf Grap hic file (type pdf) <use 5_home_rshepard_projects_washington_nevins-dock_analyses_current.pdf> Package pdftex.def Info: 5_home_rshepard_projects_washington_nevins-dock_analys es_current.pdf used on input line 491. (pdftex.def) Requested size: 483.67337pt x 483.69922pt. <6_home_rshepard_projects_washington_nevins-dock_analyses_discharge.pdf, id=78, 433.62pt x 433.62pt> File: 6_home_rshepard_projects_washington_nevins-dock_analyses_discharge.pdf Gr aphic file (type pdf) <use 6_home_rshepard_projects_washington_nevins-dock_analyses_discharge.pdf> Package pdftex.def Info: 6_home_rshepard_projects_washington_nevins-dock_analys es_discharge.pdf used on input line 500. (pdftex.def) Requested size: 483.67337pt x 483.69922pt. <7_home_rshepard_projects_washington_nevins-dock_analyses_stage.pdf, id=80, 433 .62pt x 433.62pt> File: 7_home_rshepard_projects_washington_nevins-dock_analyses_stage.pdf Graphi c file (type pdf) <use 7_home_rshepard_projects_washington_nevins-dock_analyses_stage.pdf> Package pdftex.def Info: 7_home_rshepard_projects_washington_nevins-dock_analys es_stage.pdf used on input line 508. (pdftex.def) Requested size: 483.67337pt x 483.69922pt. <8_home_rshepard_projects_washington_nevins-dock_analyses_suspended-sediments.p df, id=82, 433.62pt x 433.62pt> File: 8_home_rshepard_projects_washington_nevins-dock_analyses_suspended-sedime nts.pdf Graphic file (type pdf) <use 8_home_rshepard_projects_washington_nevins-dock_analyses_suspended-sedimen ts.pdf> Package pdftex.def Info: 8_home_rshepard_projects_washington_nevins-dock_analys es_suspended-sediments.pdf used on input line 529. (pdftex.def) Requested size: 483.67337pt x 483.69922pt. <9_home_rshepard_projects_washington_nevins-dock_analyses_turbidity.pdf, id=84, 433.62pt x 433.62pt> File: 9_home_rshepard_projects_washington_nevins-dock_analyses_turbidity.pdf Gr aphic file (type pdf) <use 9_home_rshepard_projects_washington_nevins-dock_analyses_turbidity.pdf> Package pdftex.def Info: 9_home_rshepard_projects_washington_nevins-dock_analys es_turbidity.pdf used on input line 537. (pdftex.def) Requested size: 483.67337pt x 483.69922pt. [11 ] [12 <./5_home_rshepard_projects_washington_nevins-dock_analyses_current.pdf>] [13 <./6_home_rshepard_projects_washington_nevins-dock_analyses_discharge.pdf>] [14 <./7_home_rshepard_projects_washington_nevins-dock_analyses_stage.pdf>] [15 ] [16 <./8_home_rshepard_projects_washington_nevins-dock_analyses_suspended-sed iments.pdf>] [17 <./9_home_rshepard_projects_washington_nevins-dock_analyses_tu rbidity.pdf>] chapter 4. Overfull \hbox (30.55435pt too wide) in paragraph at lines 567--567 [][]$\T1/cmtt/m/n/9 https : / / www . columbiacommunityconnection . com / the -[]dalles / high-[]water-[]temps-[]killing-[]fish-[]in-[]the-[]columbia-[]river $| [] LaTeX Warning: Citation 'Poole2001' on page 18 undefined on input line 571. [18 ] chapter 5. [19 ] chapter 6. LaTeX Warning: Empty bibliography on input line 616. [20 ] LaTeX3 Info: Redefining command \BeforeClosingMainAux with sig. 'm' on line (LaTeX3) 618. LaTeX3 Info: Redefining command \BeforeClosingMainAux with sig. 'm' on line (LaTeX3) 618. LaTeX3 Info: Redefining command \BeforeClosingMainAux with sig. 'm' on line (LaTeX3) 618. LaTeX3 Info: Redefining command \BeforeClosingMainAux with sig. 'm' on line (LaTeX3) 618. (./biological-evaluation.aux) LaTeX Warning: There were undefined references. Package biblatex Warning: Please (re)run Biber on the file: (biblatex) biological-evaluation (biblatex) and rerun LaTeX afterwards. Package logreq Info: Writing requests to 'biological-evaluation.run.xml'. \openout1 = `biological-evaluation.run.xml'. ) Here is how much of TeX's memory you used: 14196 strings out of 478994 300509 string characters out of 5864719 1140503 words of memory out of 5000000 31514 multiletter control sequences out of 15000+600000 437317 words of font info for 94 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 111i,21n,116p,10660b,1191s stack positions out of 5000i,500n,10000p,200000b,80000s </home/rshepard/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt0900. 600pk> </home/rshepard/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1 200.600pk>{/usr/share/texmf-dist/fonts/enc/dvips/base/8r.enc} </home/rshepard/. texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1440.600pk> </home/rshepa rd/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx1095.600pk> </home/rs hepard/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecsx2074.600pk></usr/ share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texmf-di st/fonts/type1/urw/palatino/uplb8a.pfb></usr/share/texmf-dist/fonts/type1/urw/p alatino/uplr8a.pfb></usr/share/texmf-dist/fonts/type1/urw/palatino/uplr8a.pfb>< /usr/share/texmf-dist/fonts/type1/urw/palatino/uplri8a.pfb> Output written on biological-evaluation.pdf (23 pages, 1899335 bytes). PDF statistics: 382 PDF objects out of 1000 (max. 8388607) 129 compressed objects within 2 object streams 0 named destinations out of 1000 (max. 500000) 94 words of extra memory for PDF output out of 10000 (max. 10000000)
-- lyx-users mailing list lyx-users@lists.lyx.org http://lists.lyx.org/mailman/listinfo/lyx-users