[adegenet-commits] r877 - in pkg/inst: . doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 25 18:40:11 CEST 2011
Author: jombart
Date: 2011-05-25 18:40:11 +0200 (Wed, 25 May 2011)
New Revision: 877
Added:
pkg/inst/doc/
pkg/inst/doc/Robjects/
pkg/inst/doc/adegenet-basics.Rnw
pkg/inst/doc/adegenet-basics.aux
pkg/inst/doc/adegenet-basics.log
pkg/inst/doc/adegenet-basics.out
pkg/inst/doc/adegenet-basics.pdf
pkg/inst/doc/adegenet-basics.tex
pkg/inst/doc/adegenet-basics.toc
pkg/inst/doc/adegenet-dapc.Rnw
pkg/inst/doc/adegenet-genomics.Rnw
pkg/inst/doc/figs/
Log:
Started making empty vignettes.
Added: pkg/inst/doc/adegenet-basics.Rnw
===================================================================
--- pkg/inst/doc/adegenet-basics.Rnw (rev 0)
+++ pkg/inst/doc/adegenet-basics.Rnw 2011-05-25 16:40:11 UTC (rev 877)
@@ -0,0 +1,42 @@
+\documentclass{article}
+% \VignettePackage{adegenet}
+% \VignetteIndexEntry{adegenet basics: analysing genetic data}
+
+\usepackage{graphicx}
+\usepackage[colorlinks=true,urlcolor=blue]{hyperref}
+\usepackage{array}
+\usepackage{color}
+
+\usepackage[utf8]{inputenc} % for UTF-8/single quotes from sQuote()
+\newcommand{\code}[1]{{{\tt #1}}}
+\title{adegenet basics: analysing genetic data}
+\author{Thibaut Jombart}
+\date{\today}
+
+
+
+
+\sloppy
+\hyphenpenalty 10000
+
+
+\begin{document}
+
+
+
+\definecolor{Soutput}{rgb}{0,0,0.56}
+\definecolor{Sinput}{rgb}{0.56,0,0}
+\DefineVerbatimEnvironment{Sinput}{Verbatim}
+{formatcom={\color{Sinput}},fontsize=\footnotesize, baselinestretch=0.75}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}
+{formatcom={\color{Soutput}},fontsize=\footnotesize, baselinestretch=0.75}
+
+\color{black}
+
+\maketitle
+\tableofcontents
+
+
+
+
+\end{document}
Added: pkg/inst/doc/adegenet-basics.aux
===================================================================
--- pkg/inst/doc/adegenet-basics.aux (rev 0)
+++ pkg/inst/doc/adegenet-basics.aux 2011-05-25 16:40:11 UTC (rev 877)
@@ -0,0 +1,13 @@
+\relax
+\ifx\hyper at anchor\@undefined
+\global \let \oldcontentsline\contentsline
+\gdef \contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global \let \oldnewlabel\newlabel
+\gdef \newlabel#1#2{\newlabelxx{#1}#2}
+\gdef \newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\let \contentsline\oldcontentsline
+\let \newlabel\oldnewlabel}
+\else
+\global \let \hyper at last\relax
+\fi
+
Added: pkg/inst/doc/adegenet-basics.log
===================================================================
--- pkg/inst/doc/adegenet-basics.log (rev 0)
+++ pkg/inst/doc/adegenet-basics.log 2011-05-25 16:40:11 UTC (rev 877)
@@ -0,0 +1,676 @@
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.4.7) 25 MAY 2011 18:18
+entering extended mode
+ %&-line parsing enabled.
+**adegenet-basics.tex
+(./adegenet-basics.tex
+LaTeX2e <2009/09/24>
+Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
+yphenation, farsi, arabic, croatian, bulgarian, ukrainian, russian, czech, slov
+ak, danish, dutch, finnish, french, basque, ngerman, german, german-x-2009-06-1
+9, ngerman-x-2009-06-19, ibycus, monogreek, greek, ancientgreek, hungarian, san
+skrit, italian, latin, latvian, lithuanian, mongolian2a, mongolian, bokmal, nyn
+orsk, romanian, irish, coptic, serbian, turkish, welsh, esperanto, uppersorbian
+, estonian, indonesian, interlingua, icelandic, kurmanji, slovenian, polish, po
+rtuguese, spanish, galician, catalan, swedish, ukenglish, pinyin, loaded.
+(/usr/share/texmf-texlive/tex/latex/base/article.cls
+Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
+(/usr/share/texmf-texlive/tex/latex/base/size10.clo
+File: size10.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
+)
+\c at part=\count79
+\c at section=\count80
+\c at subsection=\count81
+\c at subsubsection=\count82
+\c at paragraph=\count83
+\c at subparagraph=\count84
+\c at figure=\count85
+\c at table=\count86
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+)
+(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
+Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV at toks@=\toks14
+)
+(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
+Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty
+Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
+)
+(/etc/texmf/tex/latex/config/graphics.cfg
+File: graphics.cfg 2009/08/28 v1.8 graphics configuration of TeX Live
+)
+Package graphics Info: Driver file: pdftex.def on input line 91.
+
+(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def
+File: pdftex.def 2010/03/12 v0.04p Graphics/color for pdfTeX
+\Gread at gobject=\count87
+))
+\Gin at req@height=\dimen103
+\Gin at req@width=\dimen104
+)
+(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
+Package: hyperref 2009/10/09 v6.79a Hypertext links for LaTeX
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty
+Package: ifpdf 2009/04/10 v2.0 Provides the ifpdf switch (HO)
+Package ifpdf Info: pdfTeX in pdf mode detected.
+)
+(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty
+Package: ifvtex 2008/11/04 v1.4 Switches for detecting VTeX and its modes (HO)
+Package ifvtex Info: VTeX not detected.
+)
+(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty
+Package: ifxetex 2009/01/23 v0.5 Provides ifxetex conditional
+)
+(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
+Package: hycolor 2009/10/02 v1.5 Code for color options of hyperref/bookmark (H
+O)
+
+(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty
+Package: xcolor-patch 2009/10/02 xcolor patch
+))
+\@linkdim=\dimen105
+\Hy at linkcounter=\count88
+\Hy at pagecounter=\count89
+
+(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def
+File: pd1enc.def 2009/10/09 v6.79a Hyperref: PDFDocEncoding definition (HO)
+)
+(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
+Package: etexcmds 2007/12/12 v1.2 Prefix for e-TeX command names (HO)
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty
+Package: infwarerr 2007/09/09 v1.2 Providing info/warning/message (HO)
+)
+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.
+)
+(/etc/texmf/tex/latex/config/hyperref.cfg
+File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
+)
+(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
+Package: kvoptions 2009/08/13 v3.4 Keyval support for LaTeX options (HO)
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty
+Package: kvsetkeys 2009/07/30 v1.5 Key value parser with default handler suppor
+t (HO)
+))
+Package hyperref Info: Option `colorlinks' set `true' on input line 2864.
+Package hyperref Info: Hyper figures OFF on input line 2975.
+Package hyperref Info: Link nesting OFF on input line 2980.
+Package hyperref Info: Hyper index ON on input line 2983.
+Package hyperref Info: Plain pages OFF on input line 2990.
+Package hyperref Info: Backreferencing OFF on input line 2995.
+
+Implicit mode ON; LaTeX internals redefined
+Package hyperref Info: Bookmarks ON on input line 3191.
+(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty
+\Urlmuskip=\muskip10
+Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.
+)
+LaTeX Info: Redefining \url on input line 3428.
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
+Package: bitset 2007/09/28 v1.0 Data type bit set (HO)
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty
+Package: intcalc 2007/09/27 v1.1 Expandable integer calculations (HO)
+)
+(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
+Package: bigintcalc 2007/11/11 v1.1 Expandable big integer calculations (HO)
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
+Package: pdftexcmds 2009/09/23 v0.6 LuaTeX support for pdfTeX utility functions
+ (HO)
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty
+Package: ifluatex 2009/04/17 v1.2 Provides the ifluatex switch (HO)
+Package ifluatex Info: LuaTeX not detected.
+)
+(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty
+Package: ltxcmds 2009/08/05 v1.0 Some LaTeX kernel commands for general use (HO
+)
+)
+Package pdftexcmds Info: LuaTeX not detected.
+Package pdftexcmds Info: \pdf at primitive is available.
+Package pdftexcmds Info: \pdf at ifprimitive is available.
+)))
+\Fld at menulength=\count90
+\Field at Width=\dimen106
+\Fld at charsize=\dimen107
+\Field at toks=\toks15
+Package hyperref Info: Hyper figures OFF on input line 4377.
+Package hyperref Info: Link nesting OFF on input line 4382.
+Package hyperref Info: Hyper index ON on input line 4385.
+Package hyperref Info: backreferencing OFF on input line 4392.
+Package hyperref Info: Link coloring ON on input line 4395.
+Package hyperref Info: Link coloring with OCG OFF on input line 4402.
+Package hyperref Info: PDF/A mode OFF on input line 4407.
+
+(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty
+Package: atbegshi 2008/07/31 v1.9 At begin shipout hook (HO)
+)
+\Hy at abspage=\count91
+\c at Item=\count92
+\c at Hfootnote=\count93
+)
+*hyperref using default driver hpdftex*
+(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def
+File: hpdftex.def 2009/10/09 v6.79a Hyperref driver for pdfTeX
+\Fld at listcount=\count94
+)
+(/usr/share/texmf-texlive/tex/latex/tools/array.sty
+Package: array 2008/09/09 v2.4c Tabular extension package (FMi)
+\col at sep=\dimen108
+\extrarowheight=\dimen109
+\NC at list=\toks16
+\extratabsurround=\skip43
+\backup at length=\skip44
+)
+(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
+Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC)
+
+(/etc/texmf/tex/latex/config/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 130.
+)
+(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
+Package: inputenc 2008/03/30 v1.1d Input encoding file
+\inpenc at prehook=\toks17
+\inpenc at posthook=\toks18
+
+(/usr/share/texmf-texlive/tex/latex/base/utf8.def
+File: utf8.def 2008/04/05 v1.1m UTF-8 support for inputenc
+Now handling font encoding OML ...
+... no UTF-8 mapping file for font encoding OML
+Now handling font encoding T1 ...
+... processing UTF-8 mapping file for font encoding T1
+
+(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu
+File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A1 (decimal 161)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00AB (decimal 171)
+ defining Unicode char U+00BB (decimal 187)
+ defining Unicode char U+00BF (decimal 191)
+ defining Unicode char U+00C0 (decimal 192)
+ defining Unicode char U+00C1 (decimal 193)
+ defining Unicode char U+00C2 (decimal 194)
+ defining Unicode char U+00C3 (decimal 195)
+ defining Unicode char U+00C4 (decimal 196)
+ defining Unicode char U+00C5 (decimal 197)
+ defining Unicode char U+00C6 (decimal 198)
+ defining Unicode char U+00C7 (decimal 199)
+ defining Unicode char U+00C8 (decimal 200)
+ defining Unicode char U+00C9 (decimal 201)
+ defining Unicode char U+00CA (decimal 202)
+ defining Unicode char U+00CB (decimal 203)
+ defining Unicode char U+00CC (decimal 204)
+ defining Unicode char U+00CD (decimal 205)
+ defining Unicode char U+00CE (decimal 206)
+ defining Unicode char U+00CF (decimal 207)
+ defining Unicode char U+00D0 (decimal 208)
+ defining Unicode char U+00D1 (decimal 209)
+ defining Unicode char U+00D2 (decimal 210)
+ defining Unicode char U+00D3 (decimal 211)
+ defining Unicode char U+00D4 (decimal 212)
+ defining Unicode char U+00D5 (decimal 213)
+ defining Unicode char U+00D6 (decimal 214)
+ defining Unicode char U+00D8 (decimal 216)
+ defining Unicode char U+00D9 (decimal 217)
+ defining Unicode char U+00DA (decimal 218)
+ defining Unicode char U+00DB (decimal 219)
+ defining Unicode char U+00DC (decimal 220)
+ defining Unicode char U+00DD (decimal 221)
+ defining Unicode char U+00DE (decimal 222)
+ defining Unicode char U+00DF (decimal 223)
+ defining Unicode char U+00E0 (decimal 224)
+ defining Unicode char U+00E1 (decimal 225)
+ defining Unicode char U+00E2 (decimal 226)
+ defining Unicode char U+00E3 (decimal 227)
+ defining Unicode char U+00E4 (decimal 228)
+ defining Unicode char U+00E5 (decimal 229)
+ defining Unicode char U+00E6 (decimal 230)
+ defining Unicode char U+00E7 (decimal 231)
+ defining Unicode char U+00E8 (decimal 232)
+ defining Unicode char U+00E9 (decimal 233)
+ defining Unicode char U+00EA (decimal 234)
+ defining Unicode char U+00EB (decimal 235)
+ defining Unicode char U+00EC (decimal 236)
+ defining Unicode char U+00ED (decimal 237)
+ defining Unicode char U+00EE (decimal 238)
+ defining Unicode char U+00EF (decimal 239)
+ defining Unicode char U+00F0 (decimal 240)
+ defining Unicode char U+00F1 (decimal 241)
+ defining Unicode char U+00F2 (decimal 242)
+ defining Unicode char U+00F3 (decimal 243)
+ defining Unicode char U+00F4 (decimal 244)
+ defining Unicode char U+00F5 (decimal 245)
+ defining Unicode char U+00F6 (decimal 246)
+ defining Unicode char U+00F8 (decimal 248)
+ defining Unicode char U+00F9 (decimal 249)
+ defining Unicode char U+00FA (decimal 250)
+ defining Unicode char U+00FB (decimal 251)
+ defining Unicode char U+00FC (decimal 252)
+ defining Unicode char U+00FD (decimal 253)
+ defining Unicode char U+00FE (decimal 254)
+ defining Unicode char U+00FF (decimal 255)
+ defining Unicode char U+0102 (decimal 258)
+ defining Unicode char U+0103 (decimal 259)
+ defining Unicode char U+0104 (decimal 260)
+ defining Unicode char U+0105 (decimal 261)
+ defining Unicode char U+0106 (decimal 262)
+ defining Unicode char U+0107 (decimal 263)
+ defining Unicode char U+010C (decimal 268)
+ defining Unicode char U+010D (decimal 269)
+ defining Unicode char U+010E (decimal 270)
+ defining Unicode char U+010F (decimal 271)
+ defining Unicode char U+0110 (decimal 272)
+ defining Unicode char U+0111 (decimal 273)
+ defining Unicode char U+0118 (decimal 280)
+ defining Unicode char U+0119 (decimal 281)
+ defining Unicode char U+011A (decimal 282)
+ defining Unicode char U+011B (decimal 283)
+ defining Unicode char U+011E (decimal 286)
+ defining Unicode char U+011F (decimal 287)
+ defining Unicode char U+0130 (decimal 304)
+ defining Unicode char U+0131 (decimal 305)
+ defining Unicode char U+0132 (decimal 306)
+ defining Unicode char U+0133 (decimal 307)
+ defining Unicode char U+0139 (decimal 313)
+ defining Unicode char U+013A (decimal 314)
+ defining Unicode char U+013D (decimal 317)
+ defining Unicode char U+013E (decimal 318)
+ defining Unicode char U+0141 (decimal 321)
+ defining Unicode char U+0142 (decimal 322)
+ defining Unicode char U+0143 (decimal 323)
+ defining Unicode char U+0144 (decimal 324)
+ defining Unicode char U+0147 (decimal 327)
+ defining Unicode char U+0148 (decimal 328)
+ defining Unicode char U+014A (decimal 330)
+ defining Unicode char U+014B (decimal 331)
+ defining Unicode char U+0150 (decimal 336)
+ defining Unicode char U+0151 (decimal 337)
+ defining Unicode char U+0152 (decimal 338)
+ defining Unicode char U+0153 (decimal 339)
+ defining Unicode char U+0154 (decimal 340)
+ defining Unicode char U+0155 (decimal 341)
+ defining Unicode char U+0158 (decimal 344)
+ defining Unicode char U+0159 (decimal 345)
+ defining Unicode char U+015A (decimal 346)
+ defining Unicode char U+015B (decimal 347)
+ defining Unicode char U+015E (decimal 350)
+ defining Unicode char U+015F (decimal 351)
+ defining Unicode char U+0160 (decimal 352)
+ defining Unicode char U+0161 (decimal 353)
+ defining Unicode char U+0162 (decimal 354)
+ defining Unicode char U+0163 (decimal 355)
+ defining Unicode char U+0164 (decimal 356)
+ defining Unicode char U+0165 (decimal 357)
+ defining Unicode char U+016E (decimal 366)
+ defining Unicode char U+016F (decimal 367)
+ defining Unicode char U+0170 (decimal 368)
+ defining Unicode char U+0171 (decimal 369)
+ defining Unicode char U+0178 (decimal 376)
+ defining Unicode char U+0179 (decimal 377)
+ defining Unicode char U+017A (decimal 378)
+ defining Unicode char U+017B (decimal 379)
+ defining Unicode char U+017C (decimal 380)
+ defining Unicode char U+017D (decimal 381)
+ defining Unicode char U+017E (decimal 382)
+ defining Unicode char U+200C (decimal 8204)
+ defining Unicode char U+2013 (decimal 8211)
+ defining Unicode char U+2014 (decimal 8212)
+ defining Unicode char U+2018 (decimal 8216)
+ defining Unicode char U+2019 (decimal 8217)
+ defining Unicode char U+201A (decimal 8218)
+ defining Unicode char U+201C (decimal 8220)
+ defining Unicode char U+201D (decimal 8221)
+ defining Unicode char U+201E (decimal 8222)
+ defining Unicode char U+2030 (decimal 8240)
+ defining Unicode char U+2031 (decimal 8241)
+ defining Unicode char U+2039 (decimal 8249)
+ defining Unicode char U+203A (decimal 8250)
+ defining Unicode char U+2423 (decimal 9251)
+)
+Now handling font encoding OT1 ...
+... processing UTF-8 mapping file for font encoding OT1
+
+(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu
+File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A1 (decimal 161)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00B8 (decimal 184)
+ defining Unicode char U+00BF (decimal 191)
+ defining Unicode char U+00C5 (decimal 197)
+ defining Unicode char U+00C6 (decimal 198)
+ defining Unicode char U+00D8 (decimal 216)
+ defining Unicode char U+00DF (decimal 223)
+ defining Unicode char U+00E6 (decimal 230)
+ defining Unicode char U+00EC (decimal 236)
+ defining Unicode char U+00ED (decimal 237)
+ defining Unicode char U+00EE (decimal 238)
+ defining Unicode char U+00EF (decimal 239)
+ defining Unicode char U+00F8 (decimal 248)
+ defining Unicode char U+0131 (decimal 305)
+ defining Unicode char U+0141 (decimal 321)
+ defining Unicode char U+0142 (decimal 322)
+ defining Unicode char U+0152 (decimal 338)
+ defining Unicode char U+0153 (decimal 339)
+ defining Unicode char U+2013 (decimal 8211)
+ defining Unicode char U+2014 (decimal 8212)
+ defining Unicode char U+2018 (decimal 8216)
+ defining Unicode char U+2019 (decimal 8217)
+ defining Unicode char U+201C (decimal 8220)
+ defining Unicode char U+201D (decimal 8221)
+)
+Now handling font encoding OMS ...
+... processing UTF-8 mapping file for font encoding OMS
+
+(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu
+File: omsenc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A7 (decimal 167)
+ defining Unicode char U+00B6 (decimal 182)
+ defining Unicode char U+00B7 (decimal 183)
+ defining Unicode char U+2020 (decimal 8224)
+ defining Unicode char U+2021 (decimal 8225)
+ defining Unicode char U+2022 (decimal 8226)
+)
+Now handling font encoding OMX ...
+... no UTF-8 mapping file for font encoding OMX
+Now handling font encoding U ...
+... no UTF-8 mapping file for font encoding U
+Now handling font encoding PD1 ...
+... no UTF-8 mapping file for font encoding PD1
+ defining Unicode char U+00A9 (decimal 169)
+ defining Unicode char U+00AA (decimal 170)
+ defining Unicode char U+00AE (decimal 174)
+ defining Unicode char U+00BA (decimal 186)
+ defining Unicode char U+02C6 (decimal 710)
+ defining Unicode char U+02DC (decimal 732)
+ defining Unicode char U+200C (decimal 8204)
+ defining Unicode char U+2026 (decimal 8230)
+ defining Unicode char U+2122 (decimal 8482)
+ defining Unicode char U+2423 (decimal 9251)
+))
+(/usr/local/R-versions/R-2.13.0/share/texmf/tex/latex/Sweave.sty
+Package: Sweave
+
+(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty
+Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
+)
+(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
+Package: fancyvrb 2008/02/07
+
+Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
+<2008/02/07> (tvz)
+\FV at CodeLineNo=\count95
+\FV at InFile=\read1
+\FV at TabBox=\box26
+\c at FancyVerbLine=\count96
+\FV at StepNumber=\count97
+\FV at OutFile=\write3
+)
+(/usr/local/R-versions/R-2.13.0/share/texmf/tex/latex/upquote.sty
+Package: upquote 2003/08/11 v1.1 Covington's upright-quote modification to verb
+atim and verb
+
+(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
+Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
+Package textcomp Info: Sub-encoding information:
+(textcomp) 5 = only ISO-Adobe without \textcurrency
+(textcomp) 4 = 5 + \texteuro
+(textcomp) 3 = 4 + \textohm
+(textcomp) 2 = 3 + \textestimated + \textcurrency
+(textcomp) 1 = TS1 - \textcircled - \t
+(textcomp) 0 = TS1 (full)
+(textcomp) Font families with sub-encoding setting implement
+(textcomp) only a restricted character set as indicated.
+(textcomp) Family '?' is the default used for unknown fonts.
+(textcomp) See the documentation for details.
+Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
+
+(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def
+File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
+Now handling font encoding TS1 ...
+... processing UTF-8 mapping file for font encoding TS1
+
+(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu
+File: ts1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A2 (decimal 162)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00A4 (decimal 164)
+ defining Unicode char U+00A5 (decimal 165)
+ defining Unicode char U+00A6 (decimal 166)
+ defining Unicode char U+00A7 (decimal 167)
+ defining Unicode char U+00A8 (decimal 168)
+ defining Unicode char U+00A9 (decimal 169)
+ defining Unicode char U+00AA (decimal 170)
+ defining Unicode char U+00AC (decimal 172)
+ defining Unicode char U+00AE (decimal 174)
+ defining Unicode char U+00AF (decimal 175)
+ defining Unicode char U+00B0 (decimal 176)
+ defining Unicode char U+00B1 (decimal 177)
+ defining Unicode char U+00B2 (decimal 178)
+ defining Unicode char U+00B3 (decimal 179)
+ defining Unicode char U+00B4 (decimal 180)
+ defining Unicode char U+00B5 (decimal 181)
+ defining Unicode char U+00B6 (decimal 182)
+ defining Unicode char U+00B7 (decimal 183)
+ defining Unicode char U+00B9 (decimal 185)
+ defining Unicode char U+00BA (decimal 186)
+ defining Unicode char U+00BC (decimal 188)
+ defining Unicode char U+00BD (decimal 189)
+ defining Unicode char U+00BE (decimal 190)
+ defining Unicode char U+00D7 (decimal 215)
+ defining Unicode char U+00F7 (decimal 247)
+ defining Unicode char U+0192 (decimal 402)
+ defining Unicode char U+02C7 (decimal 711)
+ defining Unicode char U+02D8 (decimal 728)
+ defining Unicode char U+02DD (decimal 733)
+ defining Unicode char U+0E3F (decimal 3647)
+ defining Unicode char U+2016 (decimal 8214)
+ defining Unicode char U+2020 (decimal 8224)
+ defining Unicode char U+2021 (decimal 8225)
+ defining Unicode char U+2022 (decimal 8226)
+ defining Unicode char U+2030 (decimal 8240)
+ defining Unicode char U+2031 (decimal 8241)
+ defining Unicode char U+203B (decimal 8251)
+ defining Unicode char U+203D (decimal 8253)
+ defining Unicode char U+2044 (decimal 8260)
+ defining Unicode char U+204E (decimal 8270)
+ defining Unicode char U+2052 (decimal 8274)
+ defining Unicode char U+20A1 (decimal 8353)
+ defining Unicode char U+20A4 (decimal 8356)
+ defining Unicode char U+20A6 (decimal 8358)
+ defining Unicode char U+20A9 (decimal 8361)
+ defining Unicode char U+20AB (decimal 8363)
+ defining Unicode char U+20AC (decimal 8364)
+ defining Unicode char U+20B1 (decimal 8369)
+ defining Unicode char U+2103 (decimal 8451)
+ defining Unicode char U+2116 (decimal 8470)
+ defining Unicode char U+2117 (decimal 8471)
+ defining Unicode char U+211E (decimal 8478)
+ defining Unicode char U+2120 (decimal 8480)
+ defining Unicode char U+2122 (decimal 8482)
+ defining Unicode char U+2126 (decimal 8486)
+ defining Unicode char U+2127 (decimal 8487)
+ defining Unicode char U+212E (decimal 8494)
+ defining Unicode char U+2190 (decimal 8592)
+ defining Unicode char U+2191 (decimal 8593)
+ defining Unicode char U+2192 (decimal 8594)
+ defining Unicode char U+2193 (decimal 8595)
+ defining Unicode char U+2329 (decimal 9001)
+ defining Unicode char U+232A (decimal 9002)
+ defining Unicode char U+2422 (decimal 9250)
+ defining Unicode char U+25E6 (decimal 9702)
+ defining Unicode char U+25EF (decimal 9711)
+ defining Unicode char U+266A (decimal 9834)
+))
+LaTeX Info: Redefining \oldstylenums on input line 266.
+Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
+Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
+Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
+Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
+Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
+Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
+Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
+Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
+Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
+Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
+Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
+Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
+Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
+Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
+Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
+Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
+Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
+Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
+Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
+Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
+Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
+Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
+Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
+Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
+
+Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
+Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
+Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
+Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
+Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
+Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
+Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 311.
+Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 312.
+Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 313.
+Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 314.
+Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 315.
+Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 316.
+Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 317.
+Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 318.
+Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 319.
+Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 320.
+Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 321.
+Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 322.
+Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 323.
+Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 324.
+Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 325.
+Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 326.
+))
+(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texmf-texlive/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+))
+(/usr/share/texmf-texlive/tex/latex/ae/ae.sty
+Package: ae 2001/02/12 1.3 Almost European Computer Modern
+
+(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texmf-texlive/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+)
+LaTeX Font Info: Try loading font information for T1+aer on input line 100.
+
+(/usr/share/texmf-texlive/tex/latex/ae/t1aer.fd
+File: t1aer.fd 1997/11/16 Font definitions for T1/aer.
+)))) (./adegenet-basics.aux)
+\openout1 = `adegenet-basics.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 24.
+LaTeX Font Info: ... okay on input line 24.
+LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 24.
+LaTeX Font Info: Try loading font information for TS1+cmr on input line 24.
+
+(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd
+File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
+)
+LaTeX Font Info: ... okay on input line 24.
+
+(/usr/share/texmf/tex/context/base/supp-pdf.mkii
+[Loading MPS to PDF converter (version 2006.09.02).]
+\scratchcounter=\count98
+\scratchdimen=\dimen110
+\scratchbox=\box27
+\nofMPsegments=\count99
+\nofMParguments=\count100
+\everyMPshowfont=\toks19
+\MPscratchCnt=\count101
+\MPscratchDim=\dimen111
+\MPnumerator=\count102
+\everyMPtoPDFconversion=\toks20
+)
+Package hyperref Info: Link coloring ON on input line 24.
+ (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
+Package: nameref 2007/05/29 v2.31 Cross-referencing by name of section
+
+(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty
+Package: refcount 2008/08/11 v3.1 Data extraction from references (HO)
+)
+\c at section@level=\count103
+)
+LaTeX Info: Redefining \ref on input line 24.
+LaTeX Info: Redefining \pageref on input line 24.
+
+(./adegenet-basics.out) (./adegenet-basics.out)
+\@outlinefile=\write4
+\openout4 = `adegenet-basics.out'.
+
+\AtBeginShipoutBox=\box28
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <12> on input line 38.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <8> on input line 38.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <6> on input line 38.
+ (./adegenet-basics.toc)
+\tf at toc=\write5
+\openout5 = `adegenet-basics.toc'.
+
+
+[1
+
+{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./adegenet-basics.aux) )
+Here is how much of TeX's memory you used:
+ 5595 strings out of 493848
+ 79617 string characters out of 1152824
+ 138759 words of memory out of 3000000
+ 8759 multiletter control sequences out of 15000+50000
+ 19449 words of font info for 44 fonts, out of 3000000 for 9000
+ 714 hyphenation exceptions out of 8191
+ 38i,6n,21p,278b,288s stack positions out of 5000i,500n,10000p,200000b,50000s
+<
+/usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/
+texmf-texlive/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf-texliv
+e/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texmf-texlive/fonts/type
+1/public/amsfonts/cm/cmr17.pfb>
+Output written on adegenet-basics.pdf (1 page, 38940 bytes).
+PDF statistics:
+ 28 PDF objects out of 1000 (max. 8388607)
+ 3 named destinations out of 1000 (max. 500000)
+ 1 words of extra memory for PDF output out of 10000 (max. 10000000)
+
Added: pkg/inst/doc/adegenet-basics.pdf
===================================================================
(Binary files differ)
Property changes on: pkg/inst/doc/adegenet-basics.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/inst/doc/adegenet-basics.tex
===================================================================
--- pkg/inst/doc/adegenet-basics.tex (rev 0)
+++ pkg/inst/doc/adegenet-basics.tex 2011-05-25 16:40:11 UTC (rev 877)
@@ -0,0 +1,43 @@
+\documentclass{article}
+% \VignettePackage{adegenet}
+% \VignetteIndexEntry{adegenet basics: analysing genetic data}
+
+\usepackage{graphicx}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 877
More information about the adegenet-commits
mailing list