This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex 2025.4.5)  16 APR 2025 11:57
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**treetimeusermanual.tex
(./treetimeusermanual.tex
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
(./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2024/06/29 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2024/06/29 v1.4n Standard LaTeX file (size option)
)
\c@part=\count196
\c@chapter=\count197
\c@section=\count198
\c@subsection=\count199
\c@subsubsection=\count266
\c@paragraph=\count267
\c@subparagraph=\count268
\c@figure=\count269
\c@table=\count270
\abovecaptionskip=\skip49
\belowcaptionskip=\skip50
\bibindent=\dimen141
)
LaTeX Info: Redefining \and on input line 35.
)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
Package: inputenc 2024/02/08 v1.3d Input encoding file
\inpenc@prehook=\toks17
\inpenc@posthook=\toks18
)
   defining Unicode char U+00A0 (decimal 160)
   defining Unicode char U+2500 (decimal 9472)
   defining Unicode char U+2502 (decimal 9474)
   defining Unicode char U+2514 (decimal 9492)
   defining Unicode char U+251C (decimal 9500)
   defining Unicode char U+2572 (decimal 9586)

(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty
Package: cmap 2021/02/06 v1.0j CMap support: searchable PDF
)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2021/04/29 v2.0v Standard LaTeX package
<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
Package: amsmath 2024/11/05 v2.17t AMS math features
\@mathmargin=\skip51

For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
Package: amstext 2021/08/26 v2.01 AMS text

(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty
File: amsgen.sty 1999/11/30 v2.0 generic functions
\@emptytoks=\toks19
\ex@=\dimen142
))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty
Package: amsbsy 1999/11/29 v1.2d Bold Symbols
\pmbraise@=\dimen143
)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty
Package: amsopn 2022/04/08 v2.04 operator names
)
\inf@bad=\count271
LaTeX Info: Redefining \frac on input line 233.
\uproot@=\count272
\leftroot@=\count273
LaTeX Info: Redefining \overline on input line 398.
LaTeX Info: Redefining \colon on input line 409.
\classnum@=\count274
\DOTSCASE@=\count275
LaTeX Info: Redefining \ldots on input line 495.
LaTeX Info: Redefining \dots on input line 498.
LaTeX Info: Redefining \cdots on input line 619.
\Mathstrutbox@=\box52
\strutbox@=\box53
LaTeX Info: Redefining \big on input line 721.
LaTeX Info: Redefining \Big on input line 722.
LaTeX Info: Redefining \bigg on input line 723.
LaTeX Info: Redefining \Bigg on input line 724.
\big@size=\dimen144
LaTeX Font Info:    Redeclaring font encoding OML on input line 742.
LaTeX Font Info:    Redeclaring font encoding OMS on input line 743.
\macc@depth=\count276
LaTeX Info: Redefining \bmod on input line 904.
LaTeX Info: Redefining \pmod on input line 909.
LaTeX Info: Redefining \smash on input line 939.
LaTeX Info: Redefining \relbar on input line 969.
LaTeX Info: Redefining \Relbar on input line 970.
\c@MaxMatrixCols=\count277
\dotsspace@=\muskip17
\c@parentequation=\count278
\dspbrk@lvl=\count279
\tag@help=\toks20
\row@=\count280
\column@=\count281
\maxfields@=\count282
\andhelp@=\toks21
\eqnshift@=\dimen145
\alignsep@=\dimen146
\tagshift@=\dimen147
\tagwidth@=\dimen148
\totwidth@=\dimen149
\lineht@=\dimen150
\@envbody=\toks22
\multlinegap=\skip52
\multlinetaggap=\skip53
\mathdisplay@stack=\toks23
LaTeX Info: Redefining \[ on input line 2953.
LaTeX Info: Redefining \] on input line 2954.
)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
Package: amssymb 2013/01/14 v3.01 AMS font symbols

(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty
Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info:    Redeclaring math symbol \hbar on input line 98.
LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
Package: babel 2025/02/14 v25.4 The multilingual framework for pdfLaTeX, LuaLaT
eX and XeLaTeX
\babel@savecnt=\count283
\U@D=\dimen151
\l@unhyphenated=\language28

(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)
\bbl@readstream=\read2
\bbl@dirlevel=\count284

(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
Language: english 2017/06/06 v3.3r English support from the babel system
Package babel Info: Hyphen rules for 'british' set to \l@english
(babel)             (\language0). Reported on input line 82.
Package babel Info: Hyphen rules for 'UKenglish' set to \l@english
(babel)             (\language0). Reported on input line 83.
Package babel Info: Hyphen rules for 'canadian' set to \l@english
(babel)             (\language0). Reported on input line 102.
Package babel Info: Hyphen rules for 'australian' set to \l@english
(babel)             (\language0). Reported on input line 105.
Package babel Info: Hyphen rules for 'newzealand' set to \l@english
(babel)             (\language0). Reported on input line 108.
))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex
Package babel Info: Importing font and identification data for english
(babel)             from babel-en.ini. Reported on input line 11.
)
(/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty
Package: tgtermes 2009/09/27 v1.2 TeX Gyre Termes as default roman family

(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
Package: kvoptions 2022-06-15 v3.15 Key value format for package options (HO)

(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2022/05/29 v1.15 key=value parser (DPC)
\KV@toks@=\toks24
)
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty
Package: ltxcmds 2023-12-04 v1.26 LaTeX kernel commands for general use (HO)
)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty
Package: kvsetkeys 2022-10-05 v1.19 Key value parser (HO)
)))
(/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty
Package: tgheros 2009/09/27 v1.2 TeX Gyre Heros as default sans serif family
)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty
Package: fncychap 2007/07/30 v1.34 LaTeX package (Revised chapters)
\RW=\skip54
\mylen=\skip55
\myhi=\skip56
\px=\skip57
\py=\skip58
\pyy=\skip59
\pxx=\skip60
\c@AlphaCnt=\count285
\c@AlphaDecCnt=\count286
) (./sphinx.sty
Package: sphinx 2024/10/11 v8.1.1 Sphinx LaTeX package (sphinx-doc)

(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
Package: xcolor 2024/09/29 v3.02 LaTeX color extensions (UK)

(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg
File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package xcolor Info: Driver file: pdftex.def on input line 274.

(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def
File: pdftex.def 2024/04/13 v1.2c Graphics/color driver for pdftex
)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)
Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1349.
Package xcolor Info: Model `hsb' substituted by `rgb' on input line 1353.
Package xcolor Info: Model `RGB' extended on input line 1365.
Package xcolor Info: Model `HTML' substituted by `rgb' on input line 1367.
Package xcolor Info: Model `Hsb' substituted by `hsb' on input line 1368.
Package xcolor Info: Model `tHsb' substituted by `hsb' on input line 1369.
Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1370.
Package xcolor Info: Model `Gray' substituted by `gray' on input line 1371.
Package xcolor Info: Model `wave' substituted by `hsb' on input line 1372.
)
(./sphinxoptionshyperref.sty
Package: sphinxoptionshyperref 2021/01/27 hyperref
) (./sphinxoptionsgeometry.sty
Package: sphinxoptionsgeometry 2021/01/27 geometry
)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
Package: textcomp 2024/04/24 v2.1b Standard LaTeX package
)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty
Package: float 2001/11/08 v1.3d Float enhancements (AL)
\c@float@type=\count287
\float@exts=\toks25
\float@box=\box54
\@float@everytoks=\toks26
\@floatcapt=\box55
)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty
\wrapoverhang=\dimen152
\WF@size=\dimen153
\c@WF@wrappedlines=\count288
\WF@box=\box56
\WF@everypar=\toks27
Package: wrapfig 2003/01/31  v 3.6
)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty
Package: capt-of 2009/12/29 v0.2 standard captions outside of floats
)
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty
Package: multicol 2024/09/14 v1.9i multicolumn formatting (FMi)
\c@tracingmulticols=\count289
\mult@box=\box57
\multicol@leftmargin=\dimen154
\c@unbalance=\count290
\c@collectmore=\count291
\doublecol@number=\count292
\multicoltolerance=\count293
\multicolpretolerance=\count294
\full@width=\dimen155
\page@free=\dimen156
\premulticols=\dimen157
\postmulticols=\dimen158
\multicolsep=\skip61
\multicolbaselineskip=\skip62
\partial@page=\box58
\last@line=\box59
\mc@boxedresult=\box60
\maxbalancingoverflow=\dimen159
\mult@rightbox=\box61
\mult@grightbox=\box62
\mult@firstbox=\box63
\mult@gfirstbox=\box64
\@tempa=\box65
\@tempa=\box66
\@tempa=\box67
\@tempa=\box68
\@tempa=\box69
\@tempa=\box70
\@tempa=\box71
\@tempa=\box72
\@tempa=\box73
\@tempa=\box74
\@tempa=\box75
\@tempa=\box76
\@tempa=\box77
\@tempa=\box78
\@tempa=\box79
\@tempa=\box80
\@tempa=\box81
\@tempa=\box82
\@tempa=\box83
\@tempa=\box84
\@tempa=\box85
\@tempa=\box86
\@tempa=\box87
\@tempa=\box88
\@tempa=\box89
\@tempa=\box90
\@tempa=\box91
\@tempa=\box92
\@tempa=\box93
\@tempa=\box94
\@tempa=\box95
\@tempa=\box96
\@tempa=\box97
\@tempa=\box98
\@tempa=\box99
\@tempa=\box100
\c@minrows=\count295
\c@columnbadness=\count296
\c@finalcolumnbadness=\count297
\last@try=\dimen160
\multicolovershoot=\dimen161
\multicolundershoot=\dimen162
\mult@nat@firstbox=\box101
\colbreak@box=\box102
\mc@col@check@num=\count298
)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR)

(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2024/08/06 v1.4g Standard LaTeX Graphics (DPC,SPQR)

(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 2023/12/02 v1.11 sin cos tan (DPC)
)
(/usr/share/texlive/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 106.
)
\Gin@req@height=\dimen163
\Gin@req@width=\dimen164
)
(./sphinxlatexgraphics.sty
Package: sphinxlatexgraphics 2024/08/13 v8.1.0 graphics
\spx@image@maxheight=\dimen165
\spx@image@box=\box103
) (./sphinxpackageboxes.sty
Package: sphinxpackageboxes 2024/07/01 v7.4.0 advanced colored boxes

(/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty
Package: pict2e 2020/09/30 v0.4b Improved picture commands (HjG,RN,JT)

(/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg
File: pict2e.cfg 2016/02/05 v0.1u pict2e configuration for teTeX/TeXLive
)
Package pict2e Info: Driver file: pdftex.def on input line 112.
Package pict2e Info: Driver file for pict2e: p2e-pdftex.def on input line 114.

(/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def
File: p2e-pdftex.def 2016/02/05 v0.1u Driver-dependant file (RN,HjG,JT)
)
\pIIe@GRAPH=\toks28
\@arclen=\dimen166
\@arcrad=\dimen167
\pIIe@tempdima=\dimen168
\pIIe@tempdimb=\dimen169
\pIIe@tempdimc=\dimen170
\pIIe@tempdimd=\dimen171
\pIIe@tempdime=\dimen172
\pIIe@tempdimf=\dimen173
)
(/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty
Package: ellipse 2004/11/05 v1.0 .dtx ellipse file
)
\@tempdimd=\dimen174
\spx@tempboxa=\box104
\spx@tempboxb=\box105
\spx@boxes@border@top=\dimen175
\spx@boxes@border@right=\dimen176
\spx@boxes@border@bottom=\dimen177
\spx@boxes@border@left=\dimen178
\spx@boxes@padding@top=\dimen179
\spx@boxes@padding@right=\dimen180
\spx@boxes@padding@bottom=\dimen181
\spx@boxes@padding@left=\dimen182
\spx@boxes@shadow@xoffset=\dimen183
\spx@boxes@shadow@yoffset=\dimen184
\spx@boxes@radius@topleft@x=\dimen185
\spx@boxes@radius@topright@x=\dimen186
\spx@boxes@radius@bottomright@x=\dimen187
\spx@boxes@radius@bottomleft@x=\dimen188
\spx@boxes@radius@topleft@y=\dimen189
\spx@boxes@radius@topright@y=\dimen190
\spx@boxes@radius@bottomright@y=\dimen191
\spx@boxes@radius@bottomleft@y=\dimen192
)
(./sphinxlatexadmonitions.sty
Package: sphinxlatexadmonitions 2024/10/11 v8.1.1 admonitions

(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty
Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks
\OuterFrameSep=\skip63
\fb@frw=\dimen193
\fb@frh=\dimen194
\FrameRule=\dimen195
\FrameSep=\dimen196
)
(./sphinxpackagefootnote.sty
Package: sphinxpackagefootnote 2024/05/17 v7.3.x Sphinx custom footnotehyper pa
ckage (Sphinx team)
\FNH@notes=\box106
\FNH@toks=\toks29
\FNH@width=\dimen197
\c@sphinxfootnotemark=\count299
)
\spx@notice@border=\dimen198
\c@sphinxtodo=\count300
) (./sphinxlatexliterals.sty
Package: sphinxlatexliterals 2024/07/01 v7.4.0 code-blocks and parsed literals

(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Package: fancyvrb 2024/01/20 4.5c verbatim text (tvz,hv)
\FV@CodeLineNo=\count301
\FV@InFile=\read3
\FV@TabBox=\box107
\c@FancyVerbLine=\count302
\FV@StepNumber=\count303
\FV@OutFile=\write3
)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty
Package: alltt 2024/07/07 v2.0g defines alltt environment
)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
Package: upquote 2012/04/19 v1.3 upright-quote and grave-accent glyphs in verba
tim
)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty
Package: needspace 2010/09/12 v1.3d reserve vertical space
)
\sphinxcontinuationbox=\box108
\sphinxvisiblespacebox=\box109
\sphinxVerbatim@TitleBox=\box110
\sphinxVerbatim@ContentsBox=\box111
)
(./sphinxlatexshadowbox.sty
Package: sphinxlatexshadowbox 2024/07/28 v8.1.0 sphinxShadowBox
) (./sphinxlatexcontainers.sty
Package: sphinxlatexcontainers 2021/05/03 containers
)
(./sphinxhighlight.sty
Package: sphinxhighlight 2022/06/30 stylesheet for highlighting with pygments
) (./sphinxlatextables.sty
Package: sphinxlatextables 2024/07/01 v7.4.0 tables

(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
Package: tabulary 2024/06/04 v0.11 tabulary package (DPC)

(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty
Package: array 2024/10/17 v2.6g Tabular extension package (FMi)
\col@sep=\dimen199
\ar@mcellbox=\box112
\extrarowheight=\dimen256
\NC@list=\toks30
\extratabsurround=\skip64
\backup@length=\skip65
\ar@cellbox=\box113
)
\TY@count=\count304
\TY@linewidth=\dimen257
\tymin=\dimen258
\tymax=\dimen259
\TY@tablewidth=\dimen260
)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty
Package: longtable 2024-10-27 v4.22 Multi-page Table package (DPC)
\LTleft=\skip66
\LTright=\skip67
\LTpre=\skip68
\LTpost=\skip69
\LTchunksize=\count305
\LTcapwidth=\dimen261
\LT@head=\box114
\LT@firsthead=\box115
\LT@foot=\box116
\LT@lastfoot=\box117
\LT@gbox=\box118
\LT@cols=\count306
\LT@rows=\count307
\c@LT@tables=\count308
\c@LT@chunks=\count309
\LT@p@ftn=\toks31
)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty
Package: varwidth 2009/03/30 ver 0.92;  Variable-width minipages
\@vwid@box=\box119
\sift@deathcycles=\count310
\@vwid@loff=\dimen262
\@vwid@roff=\dimen263
)
\sphinx@TY@tablewidth=\dimen264

(/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty
Package: colortbl 2024/07/06 v1.0i Color table columns (DPC)
\everycr=\toks32
\minrowclearance=\skip70
\rownum=\count311
)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty
Package: booktabs 2020/01/12 v1.61803398 Publication quality tables
\heavyrulewidth=\dimen265
\lightrulewidth=\dimen266
\cmidrulewidth=\dimen267
\belowrulesep=\dimen268
\belowbottomsep=\dimen269
\aboverulesep=\dimen270
\abovetopsep=\dimen271
\cmidrulesep=\dimen272
\cmidrulekern=\dimen273
\defaultaddspace=\dimen274
\@cmidla=\count312
\@cmidlb=\count313
\@aboverulesep=\dimen275
\@belowrulesep=\dimen276
\@thisruleclass=\count314
\@lastruleclass=\count315
\@thisrulewidth=\dimen277
))
(./sphinxlatexnumfig.sty
Package: sphinxlatexnumfig 2024/07/31 v8.1.0 numbering
) (./sphinxlatexlists.sty
Package: sphinxlatexlists 2021/12/20 lists
\spx@lineitemlabel=\toks33
)
\c@sphinxscope=\count316
 (./sphinxlatexindbibtoc.sty
Package: sphinxlatexindbibtoc 2021/01/27 index, bib., toc

(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty
Package: makeidx 2021/10/04 v1.0m Standard LaTeX package
))
(./sphinxlatexstylepage.sty
Package: sphinxlatexstylepage 2021/01/27 page styling

(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty
Package: parskip 2021-03-14 v2.0h non-zero parskip adjustments

(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty
Package: etoolbox 2025/02/11 v2.5l e-TeX tools for LaTeX (JAW)
\etb@tempcnta=\count317
))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty
Package: fancyhdr 2025/02/07 v5.2 Extensive control of page headers and footers

\f@nch@headwidth=\skip71
\f@nch@offset@elh=\skip72
\f@nch@offset@erh=\skip73
\f@nch@offset@olh=\skip74
\f@nch@offset@orh=\skip75
\f@nch@offset@elf=\skip76
\f@nch@offset@erf=\skip77
\f@nch@offset@olf=\skip78
\f@nch@offset@orf=\skip79
\f@nch@height=\skip80
\f@nch@footalignment=\skip81
\f@nch@widthL=\skip82
\f@nch@widthC=\skip83
\f@nch@widthR=\skip84
\@temptokenb=\toks34
))
(./sphinxlatexstyleheadings.sty
Package: sphinxlatexstyleheadings 2023/02/11 headings

(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty
Package: titlesec 2025/01/04 v2.17 Sectioning titles
\ttl@box=\box120
\beforetitleunit=\skip85
\aftertitleunit=\skip86
\ttl@plus=\dimen278
\ttl@minus=\dimen279
\ttl@toksa=\toks35
\titlewidth=\dimen280
\titlewidthlast=\dimen281
\titlewidthfirst=\dimen282
))
(./sphinxlatexstyletext.sty
Package: sphinxlatexstyletext 2024/07/28 v8.1.0 text styling
) (./sphinxlatexobjects.sty
Package: sphinxlatexobjects 2023/07/23 documentation environments
\sphinxsignaturesep=\skip87
\sphinxsignaturelistskip=\skip88
\py@argswidth=\skip89
\lineblockindentation=\skip90
\DUlineblockindent=\skip91
))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2020/01/02 v5.9 Page Geometry

(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead.

(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty
Package: iftex 2024/12/12 v1.0g TeX engine tests
))
\Gm@cnth=\count318
\Gm@cntv=\count319
\c@Gm@tempcnt=\count320
\Gm@bindingoffset=\dimen283
\Gm@wd@mp=\dimen284
\Gm@odd@mp=\dimen285
\Gm@even@mp=\dimen286
\Gm@layoutwidth=\dimen287
\Gm@layoutheight=\dimen288
\Gm@layouthoffset=\dimen289
\Gm@layoutvoffset=\dimen290
\Gm@dimlist=\toks36
)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
Package: hyperref 2024-11-05 v7.01l Hypertext links for LaTeX

(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty
Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO)
)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty
Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO)

(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
Package: pdftexcmds 2020-06-27 v0.33 Utility functions of pdfTeX for LuaTeX (HO
)

(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty
Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO)
)
Package pdftexcmds Info: \pdf@primitive is available.
Package pdftexcmds Info: \pdf@ifprimitive is available.
Package pdftexcmds Info: \pdfdraftmode found.
))
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty
Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
Package: nameref 2023-11-26 v2.56 Cross-referencing by name of section

(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty
Package: refcount 2019/12/15 v3.6 Data extraction from label references (HO)
)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
Package: gettitlestring 2019/12/15 v1.6 Cleanup title references (HO)
)
\c@section@level=\count321
)
(/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty
Package: stringenc 2019/11/29 v1.12 Convert strings between diff. encodings (HO
)
)
\@linkdim=\dimen291
\Hy@linkcounter=\count322
\Hy@pagecounter=\count323

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def
File: pd1enc.def 2024-11-05 v7.01l Hyperref: PDFDocEncoding definition (HO)
Now handling font encoding PD1 ...
... no UTF-8 mapping file for font encoding PD1
)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty
Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO)
)
\Hy@SavedSpaceFactor=\count324

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def
File: puenc.def 2024-11-05 v7.01l Hyperref: PDF Unicode definition (HO)
Now handling font encoding PU ...
... no UTF-8 mapping file for font encoding PU
)
Package hyperref Info: Option `unicode' set `true' on input line 4040.
Package hyperref Info: Option `colorlinks' set `true' on input line 4040.
Package hyperref Info: Option `breaklinks' set `true' on input line 4040.
Package hyperref Info: Hyper figures OFF on input line 4157.
Package hyperref Info: Link nesting OFF on input line 4162.
Package hyperref Info: Hyper index ON on input line 4165.
Package hyperref Info: Plain pages OFF on input line 4172.
Package hyperref Info: Backreferencing OFF on input line 4177.
Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
Package hyperref Info: Bookmarks ON on input line 4424.
\c@Hy@tempcnt=\count325

(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty
\Urlmuskip=\muskip18
Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
)
LaTeX Info: Redefining \url on input line 4763.
\XeTeXLinkMargin=\dimen292

(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO)

(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty
Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO
)
))
\Fld@menulength=\count326
\Field@Width=\dimen293
\Fld@charsize=\dimen294
Package hyperref Info: Hyper figures OFF on input line 6042.
Package hyperref Info: Link nesting OFF on input line 6047.
Package hyperref Info: Hyper index ON on input line 6050.
Package hyperref Info: backreferencing OFF on input line 6057.
Package hyperref Info: Link coloring ON on input line 6060.
Package hyperref Info: Link coloring with OCG OFF on input line 6067.
Package hyperref Info: PDF/A mode OFF on input line 6072.

(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty
Package: atbegshi-ltx 2021/01/10 v1.0c Emulation of the original atbegshi
package with kernel methods
)
\Hy@abspage=\count327
\c@Item=\count328
\c@Hfootnote=\count329
)
Package hyperref Info: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
File: hpdftex.def 2024-11-05 v7.01l Hyperref driver for pdfTeX

(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty
Package: atveryend-ltx 2020/08/19 v1.0a Emulation of the original atveryend pac
kage
with kernel methods
)
\Fld@listcount=\count330
\c@bookmark@seq@number=\count331

(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
Package: rerunfilecheck 2022-07-10 v1.10 Rerun checks for auxiliary files (HO)

(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
Package: uniquecounter 2019/12/15 v1.4 Provide unlimited unique counter (HO)
)
Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
85.
)
\Hy@SectionHShift=\skip92
)
(/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty
Package: hypcap 2024-07-26 v1.13 Adjusting the anchors of captions (HO)

(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty
Package: letltxmacro 2019/12/03 v1.6 Let assignment for LaTeX macros (HO)
))
(./sphinxmessages.sty
Package: sphinxmessages 2019/01/04 v2.0 Localized LaTeX macros (Sphinx team)
)
\@indexfile=\write4
\openout4 = `treetimeusermanual.idx'.


Writing index file treetimeusermanual.idx
LaTeX Font Info:    Trying to load font information for T1+qtm on input line 72
.
(/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd
File: t1qtm.fd 2009/09/25 v1.2 font definition file for T1/qtm
)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def
File: l3backend-pdftex.def 2024-05-08 L3 backend support: PDF output (pdfTeX)
\l__color_backend_stack_int=\count332
\l__pdf_internal_box=\box121
)
(./treetimeusermanual.aux)
\openout1 = `treetimeusermanual.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.
LaTeX Font Info:    Checking defaults for PU/pdf/m/n on input line 72.
LaTeX Font Info:    ... okay on input line 72.

(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count333
\scratchdimen=\dimen295
\scratchbox=\box122
\nofMPsegments=\count334
\nofMParguments=\count335
\everyMPshowfont=\toks37
\MPscratchCnt=\count336
\MPscratchDim=\dimen296
\MPnumerator=\count337
\makeMPintoPDFobject=\count338
\everyMPtoPDFconversion=\toks38
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf
Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4
85.

(/usr/share/texlive/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
))
(/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/fontawesome5.sty
(/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.sty
Package: expl3 2025-01-18 L3 programming layer (loader) 
)
Package: fontawesome5 2022/05/02 v5.15.4 Font Awesome 5

(/usr/share/texlive/texmf-dist/tex/latex/l3packages/l3keys2e/l3keys2e.sty
Package: l3keys2e 2024-08-16 LaTeX2e option processing using LaTeX3 keys
)
(/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty
Package: xparse 2024-08-16 L3 Experimental document command parser
)
(/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/fontawesome5-generic-help
er.sty
Package: fontawesome5-generic-helper 2022/05/02 v5.15.4 non-uTeX helper for fon
tawesome5

(/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/fontawesome5-mapping.def)
))
\c@literalblock=\count339

*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*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)=(72.26999pt, 469.75502pt, 72.26999pt)
* v-part:(T,H,B)=(72.26999pt, 650.43001pt, 72.26999pt)
* \paperwidth=614.295pt
* \paperheight=794.96999pt
* \textwidth=469.75502pt
* \textheight=650.43001pt
* \oddsidemargin=0.0pt
* \evensidemargin=0.0pt
* \topmargin=-37.0pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=36.135pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt 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)

Package hyperref Info: Link coloring ON on input line 72.
(./treetimeusermanual.out) (./treetimeusermanual.out)
\@outlinefile=\write5
\openout5 = `treetimeusermanual.out'.

Package hyperref Info: Option `pageanchor' set `false' on input line 80.
LaTeX Font Info:    Trying to load font information for T1+qhv on input line 80
.

(/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd
File: t1qhv.fd 2009/09/25 v1.2 font definition file for T1/qhv
)<<ot1.cmap>><<oml.cmap>><<oms.cmap>><<omx.cmap>>
LaTeX Font Info:    Trying to load font information for U+msa on input line 80.

 (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd
File: umsa.fd 2013/01/14 v3.01 AMS symbols A
)
LaTeX Font Info:    Trying to load font information for U+msb on input line 80.


(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
)

[1

{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texmf/fonts/enc/
dvips/tex-gyre/q-ec.enc}]

[2


] (./treetimeusermanual.toc

[1

])
\tf@toc=\write6
\openout6 = `treetimeusermanual.toc'.



[2]
<treetime-logo.png, id=315, 185.0112pt x 185.0112pt>
LaTeX Font Info:    Trying to load font information for T1+txtt on input line 8
5.
 (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
File: t1txtt.fd 2000/12/15 v3.1
)
File: treetime-logo.png Graphic file (type png)
<use treetime-logo.png>
Package pdftex.def Info: treetime-logo.png  used on input line 85.
(pdftex.def)             Requested size: 92.50537pt x 92.50537pt.


[1

 <./treetime-logo.png>]

[2

]
Chapter 1.
<linked-trees1.png, id=327, 786.46765pt x 354.26471pt>
File: linked-trees1.png Graphic file (type png)
<use linked-trees1.png>
Package pdftex.def Info: linked-trees1.png  used on input line 135.
(pdftex.def)             Requested size: 469.76013pt x 211.60907pt.


[3]
<abcde011.png, id=333, 524.71031pt x 163.3603pt>
File: abcde011.png Graphic file (type png)
<use abcde011.png>
Package pdftex.def Info: abcde011.png  used on input line 151.
(pdftex.def)             Requested size: 469.76892pt x 146.25017pt.
<abcde021.png, id=334, 524.71031pt x 163.3603pt>
File: abcde021.png Graphic file (type png)
<use abcde021.png>
Package pdftex.def Info: abcde021.png  used on input line 156.
(pdftex.def)             Requested size: 469.76892pt x 146.25017pt.


[4 <./linked-trees1.png> <./abcde011.png (PNG copy)> <./abcde021.png (PNG copy)
>]
<screenshot011.png, id=339, 1293.33188pt x 733.23938pt>
File: screenshot011.png Graphic file (type png)
<use screenshot011.png>
Package pdftex.def Info: screenshot011.png  used on input line 182.
(pdftex.def)             Requested size: 469.7434pt x 266.3267pt.
<screenshot021.png, id=341, 1293.33188pt x 733.23938pt>
File: screenshot021.png Graphic file (type png)
<use screenshot021.png>
Package pdftex.def Info: screenshot021.png  used on input line 187.
(pdftex.def)             Requested size: 469.7434pt x 266.3267pt.


[5 <./screenshot011.png>]
<screenshot031.png, id=347, 793.46437pt x 336.50719pt>
File: screenshot031.png Graphic file (type png)
<use screenshot031.png>
Package pdftex.def Info: screenshot031.png  used on input line 198.
(pdftex.def)             Requested size: 469.7623pt x 199.22556pt.
<screenshot041.png, id=348, 969.6225pt x 578.16pt>
File: screenshot041.png Graphic file (type png)
<use screenshot041.png>
Package pdftex.def Info: screenshot041.png  used on input line 206.
(pdftex.def)             Requested size: 469.7633pt x 280.0985pt.


[6 <./screenshot021.png> <./screenshot031.png (PNG copy)>]
LaTeX Font Info:    Trying to load font information for TS1+qtm on input line 2
29.

(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
)

[7{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} <./screenshot041.png (P
NG copy)>]

[8]
Chapter 2.


[9

]

[10]

[11]

[12]
Chapter 3.

Underfull \hbox (badness 5274) in paragraph at lines 516--519
\T1/txtt/m/n/10 ..., "name2": ..., "name3": ...}\T1/qtm/m/n/10 , and their type
 as well as their de-fault value are the dic-
 []



[13

]

[14]
Chapter 4.


[15

]

[16]

[17]

[18]

[19]

[20

]
Chapter 5.


[21]

[22]

[23]
No file treetimeusermanual.ind.


[24] (./treetimeusermanual.aux)
 ***********
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
 ***********
Package rerunfilecheck Info: File `treetimeusermanual.out' has not changed.
(rerunfilecheck)             Checksum: A6602970205C9145DB5EE94A26741421;6378.
 ) 
Here is how much of TeX's memory you used:
 20400 strings out of 474658
 363541 string characters out of 5755528
 800791 words of memory out of 5000000
 43058 multiletter control sequences out of 15000+600000
 615090 words of font info for 77 fonts, out of 8000000 for 9000
 265 hyphenation exceptions out of 8191
 72i,12n,82p,1207b,707s stack positions out of 10000i,1000n,20000p,200000b,200000s
</usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb></usr/share/texmf/font
s/type1/public/tex-gyre/qhvbi.pfb></usr/share/texmf/fonts/type1/public/tex-gyre
/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmbi.pfb></usr/share/t
exmf/fonts/type1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/public/
tex-gyre/qtmri.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1
xtt.pfb>
Output written on treetimeusermanual.pdf (28 pages, 748883 bytes).
PDF statistics:
 500 PDF objects out of 1000 (max. 8388607)
 441 compressed objects within 5 object streams
 97 named destinations out of 1000 (max. 500000)
 549 words of extra memory for PDF output out of 10000 (max. 10000000)

