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[][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (62.123pt too wide) in paragraph at lines 182--184 [][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (56.72299pt too wide) in paragraph at lines 190--191 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ] [] Overfull \hbox (110.72308pt too wide) in paragraph at lines 194--195 [][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (105.32307pt too wide) in paragraph at lines 195--196 [][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (450.92366pt too wide) in paragraph at lines 196--199 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (164.72318pt too wide) in paragraph at lines 210--211 [][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (83.72304pt too wide) in paragraph at lines 212--213 [][][][][][][][][][][][][][][][][][][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 222--224 [][][][][][] [] Overfull \hbox (180.9232pt too wide) in paragraph at lines 222--224 [][][][][][][][] [] Overfull \hbox (137.72313pt too wide) in paragraph at lines 232--234 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (137.72313pt too wide) in paragraph at lines 236--238 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (99.92307pt too wide) in paragraph at lines 240--241 [][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (1185.3249pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (634.52397pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][] [] Overfull \hbox (62.123pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (35.12296pt too wide) in paragraph at lines 249--251 [][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (224.12328pt too wide) in paragraph at lines 251--253 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (413.1236pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (580.52388pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (2724.32751pt too wide) in paragraph at lines 266--268 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (2378.72693pt too wide) in paragraph at lines 268--270 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (3275.12845pt too wide) in paragraph at lines 270--272 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][] [] Overfull \hbox (1590.32559pt too wide) in paragraph at lines 274--276 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][] [] Overfull \hbox (1125.9248pt too wide) in paragraph at lines 276--278 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][] [] Overfull \hbox (2238.32669pt too wide) in paragraph at lines 278--280 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][] [] Overfull \hbox (1595.7256pt too wide) in paragraph at lines 280--282 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (1088.12474pt too wide) in paragraph at lines 282--284 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][] [] Overfull \hbox (1563.32555pt too wide) in paragraph at lines 284--286 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][] [] Overfull \hbox (202.52324pt too wide) in paragraph at lines 286--288 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (2.7229pt too wide) in paragraph at lines 289--291 [][][][][][][][][][][][][][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 299--301 [][][][][][] [] Overfull \hbox (170.12318pt too wide) in paragraph at lines 299--301 [][][][][][] [] Overfull \hbox (677.72404pt too wide) in paragraph at lines 303--305 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (2168.12657pt too wide) in paragraph at lines 309--311 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (56.72299pt too wide) in paragraph at lines 312--313 [][][][][][][][][][][][][][][][][] [] Overfull \hbox (143.12314pt too wide) in paragraph at lines 313--314 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (494.12373pt too wide) in paragraph at lines 327--329 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (29.72295pt too wide) in paragraph at lines 330--331 [][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (56.72299pt too wide) in paragraph at lines 331--332 [][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (89.12305pt too wide) in paragraph at lines 334--336 [][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (40.52296pt too wide) in paragraph at lines 336--337 [][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (78.32303pt too wide) in paragraph at lines 344--345 [][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (51.32298pt too wide) in paragraph at lines 345--346 [][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (326.72345pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (461.72368pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][] [] Overfull \hbox (180.9232pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (180.9232pt too wide) in paragraph at lines 351--352 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paragraph at lines 371--881 [][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (9.41107pt too wide) in paragraph at lines 881--881 [][] [] ! Extra }, or forgotten \endgroup. l.882 } I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.883 \item[\code{tikzMetricsDictionary}] { When using the graphics device pr... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 883 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (116.1231pt too wide) in paragraph at lines 1--887 [][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (71.9115pt too wide) in paragraph at lines 887--887 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.890 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass decl... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 890 [][] [] Underfull \hbox (badness 1783) in paragraph at lines 890--891 []\OT1/cmr/m/n/10 A string. The doc-u-ment-class dec-la-ra-tion when [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (105.32307pt too wide) in paragraph at lines 1--894 [][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (9.41107pt too wide) in paragraph at lines 894--894 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.896 \item[\code{tikzFooter}] {A character vector. The footer to be used onl... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 896 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (13.52292pt too wide) in paragraph at lines 1--900 [][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (9.41107pt too wide) in paragraph at lines 900--900 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.902 \item[\code{tikzLatexPackages}] { A character vector. These are the pac... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 902 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst Overfull \hbox (2.7229pt too wide) in paragraph at lines 3--4 [][][][][][][][][][][][][][][][] [] ) Overfull \hbox (9.41107pt too wide) in paragraph at lines 910--910 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 917--917 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.920 \item[\code{tikzMetricPackages}] { A character vector. These are the ex... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 920 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 928--928 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.931 \item[\code{tikzSanitizeCharacters}] {A character vector of special lat... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 931 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (78.32303pt too wide) in paragraph at lines 1--935 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (9.41107pt too wide) in paragraph at lines 935--935 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.937 \item[\code{tikzReplacementCharacters}] {A character vector of replacem... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 937 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (132.32312pt too wide) in paragraph at lines 1--941 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (9.41107pt too wide) in paragraph at lines 941--941 [][] [] ! LaTeX Error: \begin{minipage} on input line 508 ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.943 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. LaTeX Warning: Reference `part:three' on page 8 undefined on input line 947. Overfull \hbox (10.21104pt too wide) in paragraph at lines 951--951 [][] [] LaTeX Warning: Reference `subsec:fontCalc' on page 8 undefined on input line 98 2. LaTeX Warning: Reference `sec:options' on page 8 undefined on input line 987. LaTeX Warning: Reference `sec:options' on page 8 undefined on input line 988. LaTeX Warning: Reference `sec:options' on page 8 undefined on input line 989. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 1079--1079 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--1085 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--1085 [] ! Missing $ inserted. $ l.1110 mtext(paste("Linear model: $R^ {2}=", I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Bad space factor (0). \@savsf l.1117 dev.off()\end{tikzCodeBlock} I allow only values in the range 1..32767 here. (./tikzDevice.lst) ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.1117 dev.off()\end{tikzCodeBlock} This error message was generated by an \errmessage command, so I can't give any explicit help. Pretend that you're Hercule Poirot: Examine all clues, and deduce the truth by order and method. Overfull \hbox (6.66594pt too wide) in paragraph at lines 1117--1117 [][] [] ! LaTeX Error: \begin{minipage} on input line 1098 ended by \end{tikzCodeBlock} . See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1117 dev.off()\end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Missing } inserted. } l.1117 dev.off()\end{tikzCodeBlock} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Missing } inserted. } l.1118 \end{minipage} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{figure} on input line 1096 ended by \end{minipage}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1118 \end{minipage} Your command was ignored. Type I to replace it with another command, or to continue without it. (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--1122 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--1122 [] \openout4 = `tikzDevice.lst'. 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too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][] [] Overfull \hbox (1112.44766pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (561.64673pt too wide) in paragraph at lines 368--370 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (145.84602pt too wide) in paragraph at lines 370--371 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Underfull \vbox (badness 10000) detected at line 1507 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 1507--1507 [][] [] Overfull \hbox (39.41106pt too wide) in paragraph at lines 1507--1507 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1509 \item[\code{tikzMetricsDictionary}] { When using the graphics device p... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1509 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1513--1513 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1516 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass dec... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1516 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1520--1520 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1522 \item[\code{tikzFooter}] {A character vector. The footer to be used on... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1522 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1526--1526 [][] [] [8pdfTeX warning (ext4): destination with the same identifier (name{figure.1}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1528 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... ] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1528 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1528 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1536--1536 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1543--1543 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1546 \item[\code{tikzMetricPackages}] { A character vector. These are the e... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1546 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1554--1554 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1557 \item[\code{tikzSanitizeCharacters}] {A character vector of special la... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1557 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1561--1561 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1563 \item[\code{tikzReplacementCharacters}] {A character vector of replace... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 1563 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1567--1567 [][] [] ! LaTeX Error: \begin{figure} on input line 506 ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1569 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. LaTeX Warning: Reference `part:three' on page 9 undefined on input line 1573. [9] Overfull \hbox (40.21104pt too wide) in paragraph at lines 1577--1577 [][] [] LaTeX Warning: Reference `subsec:fontCalc' on page 10 undefined on input line 1 608. [10] LaTeX Warning: Reference `sec:options' on page 11 undefined on input line 1613. LaTeX Warning: Reference `sec:options' on page 11 undefined on input line 1614. LaTeX Warning: Reference `sec:options' on page 11 undefined on input line 1615. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! [11] Overfull \hbox (45.69058pt too wide) in paragraph at lines 1672--1678 []\OT1/cmr/m/n/10 <>= re-quire(tikzDevice) tikz(' simpleEx.tex',width=3.5,height=3.5) plot(1,main='Hello [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 1705--1705 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--1711 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--1711 [] Underfull \hbox (badness 10000) in paragraph at lines 1725--1729 []\OT1/cmr/m/n/10 <>= [] Underfull \hbox (badness 10000) in paragraph at lines 1725--1729 \OT1/cmr/m/n/10 re-quire(tikzDevice) tikz('latexEx.tex', [] ! Missing $ inserted. $ l.1736 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Underfull \hbox (badness 4416) in paragraph at lines 1733--1736 []\OT1/cmr/m/n/10 model <- lm(y x) rsq <- sum-mary( model [] Underfull \hbox (badness 7814) in paragraph at lines 1740--1742 []\OT1/cmr/m/n/10 mtext(paste("Linear model: $\OML/cmm/m/it/10 R[] \OT1/cmr/m/n /10 = "\OML/cmm/m/it/10 ; rsq; \OT1/cmr/m/n/10 "$" [] Underfull \hbox (badness 10000) in paragraph at lines 1743--1748 []\OT1/cmr/m/n/10 legend('bottomright', leg-end = paste("$\OML/cmm/m/it/10 y \O T1/cmr/m/n/10 = [] Overfull \hbox (30.89163pt too wide) in paragraph at lines 1743--1748 \OT1/cmr/m/n/10 "\OML/cmm/m/it/10 ; round\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef \OT1/cmr/m/n/10 (\OML/cmm/m/it/10 model\OT1/cmr/m/n/10 )[2]\OML/cmm/m/it/10 ; \ OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[] x\OT1/cmr/m/n/10 +[]\OML/cmm/m/it/10 ; ro und\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 mode l\OT1/cmr/m/n/10 )[1]\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[]$ \OT1/cmr/m/n/10 ', [] (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--1755 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--1755 [] [12pdfTeX warning (ext4): destination with the same identifier (name{figure.4}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1758 ] ! Bad space factor (0). \@savsf l.1775 dev.off()\end{tikzCodeBlock} I allow only values in the range 1..32767 here. ! Extra \endgroup. \tikzCode@suspendOutputCapture ...phack \endgroup l.1775 dev.off()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (160.77408pt too wide) in paragraph at lines 1768--1775 []\OT1/cmr/m/n/10 <>= re-qu ire(tikzDevice) tikz('bareBonesExample.tex',width=4,height=4,bareBones=T) [] (./tikzDevice.lst) ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.1775 dev.off()\end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (6.66594pt too wide) in paragraph at lines 1775--1775 [][] [] [13pdfTeX warning (ext4): destination with the same identifier (name{figure.5}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1775 dev.off()\end{tikzCodeBlock} ] ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.1775 dev.off()\end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (36.66594pt too wide) in paragraph at lines 1775--1775 [][] [] ! LaTeX Error: \begin{document} ended by \end{tikzCodeBlock}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1775 dev.off()\end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.1775 dev.off()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 1808--1808 [][] [] (./figs/bareBonesExample.tex) [14] Overfull \hbox (31.16272pt too wide) in paragraph at lines 1851--1852 \OT1/cmr/m/n/10 de-signed to be com-piled on its own. This means that in ad-di- tion to []\OT1/pcrs/m/n/10 \begin{tikzpicture} \OT1/cmr/m/n/10 and []\OT1/pcrs/ m/n/10 \end{tikzpicture} [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst Overfull \hbox (75.6459pt too wide) in paragraph at lines 117--119 [][][][][][][][][][][][] [] Overfull \hbox (216.04614pt too wide) in paragraph at lines 196--199 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (113.44597pt too wide) in paragraph at lines 222--224 [][][][][][][][][][][][][][] [] Overfull \hbox (950.44739pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (399.64645pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][] [] Overfull \hbox (178.24608pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (345.64636pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (2489.45pt too wide) in paragraph at lines 266--268 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (2143.84941pt too wide) in paragraph at lines 268--270 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (3040.25093pt too wide) in paragraph at lines 270--272 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][] [] Overfull \hbox (1355.44807pt too wide) in paragraph at lines 274--276 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 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][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (853.24722pt too wide) in paragraph at lines 282--284 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][] [] Overfull \hbox (1328.44803pt too wide) in paragraph at lines 284--286 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][] [] Overfull \hbox (102.64595pt too wide) in paragraph at lines 299--301 [][][][][][][][][][][][] [] Overfull \hbox (442.84653pt too wide) in paragraph at lines 303--305 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (1933.24905pt too wide) in paragraph at lines 309--311 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (259.24622pt too wide) in paragraph at lines 327--329 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (91.84593pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (226.84616pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][] [] Overfull \hbox (523.84666pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][] [] Overfull \hbox (1112.44766pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (561.64673pt too wide) in paragraph at lines 368--370 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (145.84602pt too wide) in paragraph at lines 370--371 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [15pdfTeX warning (ext4): destination with the same identifier (name{figure.6}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.2225 \end{tikzCodeBlock} ] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [16] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [17] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [18] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [19] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [20] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [21] Underfull \vbox (badness 10000) detected at line 2225 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2225--2225 [][] [] [22] Overfull \hbox (39.41106pt too wide) in paragraph at lines 2225--2225 [][] [] ! Too many }'s. l.2226 } You've closed more groups than you opened. Such booboos are generally harmless, so keep going. ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2227 \item[\code{tikzMetricsDictionary}] { When using the graphics device p... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2227 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2231--2231 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2234 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass dec... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2234 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2238--2238 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2240 \item[\code{tikzFooter}] {A character vector. The footer to be used on... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2240 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2244--2244 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2246 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2246 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [23] Overfull \hbox (39.41106pt too wide) in paragraph at lines 2254--2254 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2261--2261 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2264 \item[\code{tikzMetricPackages}] { A character vector. These are the e... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2264 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2272--2272 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2275 \item[\code{tikzSanitizeCharacters}] {A character vector of special la... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2275 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2279--2279 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2281 \item[\code{tikzReplacementCharacters}] {A character vector of replace... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 2281 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2285--2285 [][] [] ! LaTeX Error: \begin{document} ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2287 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.2287 \end{description} Things are pretty mixed up, but I think the worst is over. LaTeX Warning: Reference `part:three' on page 24 undefined on input line 2291. Overfull \hbox (40.21104pt too wide) in paragraph at lines 2295--2295 [][] [] [24] LaTeX Warning: Reference `subsec:fontCalc' on page 25 undefined on input line 2 326. LaTeX Warning: Reference `sec:options' on page 25 undefined on input line 2331. [25] LaTeX Warning: Reference `sec:options' on page 26 undefined on input line 2332. LaTeX Warning: Reference `sec:options' on page 26 undefined on input line 2333. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! [26] Overfull \hbox (45.69058pt too wide) in paragraph at lines 2390--2396 []\OT1/cmr/m/n/10 <>= re-quire(tikzDevice) tikz(' simpleEx.tex',width=3.5,height=3.5) plot(1,main='Hello [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 2423--2423 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--2429 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--2429 [] Underfull \hbox (badness 10000) in paragraph at lines 2443--2447 []\OT1/cmr/m/n/10 <>= [] Underfull \hbox (badness 10000) in paragraph at lines 2443--2447 \OT1/cmr/m/n/10 re-quire(tikzDevice) tikz('latexEx.tex', [] ! Missing $ inserted. $ l.2454 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Underfull \hbox (badness 4416) in paragraph at lines 2451--2454 []\OT1/cmr/m/n/10 model <- lm(y x) rsq <- sum-mary( model [] Underfull \hbox (badness 7814) in paragraph at lines 2458--2460 []\OT1/cmr/m/n/10 mtext(paste("Linear model: $\OML/cmm/m/it/10 R[] \OT1/cmr/m/n /10 = "\OML/cmm/m/it/10 ; rsq; \OT1/cmr/m/n/10 "$" [] Underfull \hbox (badness 10000) in paragraph at lines 2461--2466 []\OT1/cmr/m/n/10 legend('bottomright', leg-end = paste("$\OML/cmm/m/it/10 y \O T1/cmr/m/n/10 = [] Overfull \hbox (30.89163pt too wide) in paragraph at lines 2461--2466 \OT1/cmr/m/n/10 "\OML/cmm/m/it/10 ; round\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef \OT1/cmr/m/n/10 (\OML/cmm/m/it/10 model\OT1/cmr/m/n/10 )[2]\OML/cmm/m/it/10 ; \ OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[] x\OT1/cmr/m/n/10 +[]\OML/cmm/m/it/10 ; ro und\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 mode l\OT1/cmr/m/n/10 )[1]\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[]$ \OT1/cmr/m/n/10 ', [] (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--2473 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--2473 [] [27pdfTeX warning (ext4): destination with the same identifier (name{figure.7}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.2476 ] Overfull \hbox (190.77408pt too wide) in paragraph at lines 2486--2489 []\OT1/cmr/m/n/10 <>= re-qu ire(tikzDevice) tikz('bareBonesExample.tex',width=4,height=4,bareBones=T) [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [28pdfTeX warning (ext4): destination with the same identifi er (name{figure.8}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.2531 \end{tikzCodeBlock} ] Overfull \hbox (39.41106pt too wide) in paragraph at lines 2531--2531 [][] [] (./figs/bareBonesExample.tex) [29] Overfull \hbox (31.16272pt too wide) in paragraph at lines 2574--2575 \OT1/cmr/m/n/10 de-signed to be com-piled on its own. This means that in ad-di- tion to []\OT1/pcrs/m/n/10 \begin{tikzpicture} \OT1/cmr/m/n/10 and []\OT1/pcrs/ m/n/10 \end{tikzpicture} [] ! Bad space factor (0). \@savsf l.2580 dev.off()\end{tikzCodeBlock} I allow only values in the range 1..32767 here. ! Extra \endgroup. \tikzCode@suspendOutputCapture ...phack \endgroup l.2580 dev.off()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (90.55171pt too wide) in paragraph at lines 2576--2580 []\OT1/cmr/m/n/10 <>= re-q uire(tikzDevice) tikz('standAloneExample.tex',standAlone=T) [] (./tikzDevice.lst) Underfull \vbox (badness 4229) detected at line 2580 [] ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.2580 dev.off()\end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (6.66594pt too wide) in paragraph at lines 2580--2580 [][] [] [30pdfTeX warning (ext4): destination with the same identifier (name{figure.9}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.2580 dev.off()\end{tikzCodeBlock} ] ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.2580 dev.off()\end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (36.66594pt too wide) in paragraph at lines 2580--2580 [][] [] ! LaTeX Error: \begin{document} ended by \end{tikzCodeBlock}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2580 dev.off()\end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.2580 dev.off()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (9.08986pt too wide) in paragraph at lines 2584--2585 []\OT1/pcrs/m/n/10 \input{} \OT1/cmr/m/n/10 com-mand! Use []\OT1/pcrs/m/n/10 \i ncludegraphics{} \OT1/cmr/m/n/10 or load the [] pack-age and use []\OT1/pcrs/m/ n/10 \includepdf{}\OT1/cmr/m/n/10 . [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 2610--2610 [][] [] [31] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Underfull \vbox (badness 1147) detected at line 2687 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 2687--2687 [][] [] [32] Overfull \hbox (39.41106pt too wide) in paragraph at lines 2687--2687 [][] [] \openout4 = `tikzDevice.lst'. (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty File: lstlang1.sty 2004/09/05 1.3 listings language file ) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty File: lstlang1.sty 2004/09/05 1.3 listings language file ) (./tikzDevice.lst) [33] Overfull \hbox (39.41106pt too wide) in paragraph at lines 2693--2693 [][] [] LaTeX Warning: Reference `fig:xelatex' on page 34 undefined on input line 2695. File: img/testXeLaTeX.pdf Graphic file (type pdf) [34pdfTeX warning (ext4): destination with the same i dentifier (name{figure.10}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.2703 \newpage <./img/testXeLaTeX.pdf>] LaTeX Warning: Reference `fig:annotation' on page 35 undefined on input line 27 06. \openout4 = `tikzDevice.lst'. (./tikzDevice.lst Overfull \hbox (75.6459pt too wide) in paragraph at lines 117--119 [][][][][][][][][][][][] [] Overfull \hbox (216.04614pt too wide) in paragraph at lines 196--199 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (113.44597pt too wide) in paragraph at lines 222--224 [][][][][][][][][][][][][][] [] Overfull \hbox (950.44739pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (399.64645pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][] [] Overfull \hbox (178.24608pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (345.64636pt too wide) in paragraph at lines 257--259 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (2489.45pt too wide) in paragraph at lines 266--268 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][] [] Overfull \hbox (2143.84941pt too wide) in paragraph at lines 268--270 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (3040.25093pt too wide) in paragraph at lines 270--272 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][] [] Overfull \hbox (1355.44807pt too wide) in paragraph at lines 274--276 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 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][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (853.24722pt too wide) in paragraph at lines 282--284 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][] [] Overfull \hbox (1328.44803pt too wide) in paragraph at lines 284--286 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][] [] Overfull \hbox (102.64595pt too wide) in paragraph at lines 299--301 [][][][][][][][][][][][] [] Overfull \hbox (442.84653pt too wide) in paragraph at lines 303--305 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (1933.24905pt too wide) in paragraph at lines 309--311 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (259.24622pt too wide) in paragraph at lines 327--329 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (91.84593pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (226.84616pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][] [] Overfull \hbox (523.84666pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][] [] Overfull \hbox (1112.44766pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (561.64673pt too wide) in paragraph at lines 368--370 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (145.84602pt too wide) in paragraph at lines 370--371 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [35] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [36] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [37] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [38] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [39] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [40] Underfull \vbox (badness 10000) detected at line 3080 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3080--3080 [][] [] [41] Overfull \hbox (39.41106pt too wide) in paragraph at lines 3080--3080 [][] [] ! Too many }'s. l.3081 } You've closed more groups than you opened. Such booboos are generally harmless, so keep going. ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3082 \item[\code{tikzMetricsDictionary}] { When using the graphics device p... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3082 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3086--3086 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3089 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass dec... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3089 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [42] Overfull \hbox (39.41106pt too wide) in paragraph at lines 3093--3093 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3095 \item[\code{tikzFooter}] {A character vector. The footer to be used on... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3095 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3099--3099 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3101 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3101 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3109--3109 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3116--3116 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3119 \item[\code{tikzMetricPackages}] { A character vector. These are the e... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3119 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3127--3127 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3130 \item[\code{tikzSanitizeCharacters}] {A character vector of special la... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3130 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [43] Overfull \hbox (39.41106pt too wide) in paragraph at lines 3134--3134 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3136 \item[\code{tikzReplacementCharacters}] {A character vector of replace... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 3136 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3140--3140 [][] [] ! LaTeX Error: \begin{document} ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3142 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.3142 \end{description} Things are pretty mixed up, but I think the worst is over. LaTeX Warning: Reference `part:three' on page 44 undefined on input line 3146. Overfull \hbox (40.21104pt too wide) in paragraph at lines 3150--3150 [][] [] [44] LaTeX Warning: Reference `subsec:fontCalc' on page 45 undefined on input line 3 181. LaTeX Warning: Reference `sec:options' on page 45 undefined on input line 3186. LaTeX Warning: Reference `sec:options' on page 45 undefined on input line 3187. LaTeX Warning: Reference `sec:options' on page 45 undefined on input line 3188. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! [45] Overfull \hbox (45.69058pt too wide) in paragraph at lines 3245--3251 []\OT1/cmr/m/n/10 <>= re-quire(tikzDevice) tikz(' simpleEx.tex',width=3.5,height=3.5) plot(1,main='Hello [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 3278--3278 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--3284 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--3284 [] [46] Underfull \hbox (badness 10000) in paragraph at lines 3298--3302 []\OT1/cmr/m/n/10 <>= [] Underfull \hbox (badness 10000) in paragraph at lines 3298--3302 \OT1/cmr/m/n/10 re-quire(tikzDevice) tikz('latexEx.tex', [] ! Missing $ inserted. $ l.3309 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Underfull \hbox (badness 4416) in paragraph at lines 3306--3309 []\OT1/cmr/m/n/10 model <- lm(y x) rsq <- sum-mary( model [] Underfull \hbox (badness 7814) in paragraph at lines 3313--3315 []\OT1/cmr/m/n/10 mtext(paste("Linear model: $\OML/cmm/m/it/10 R[] \OT1/cmr/m/n /10 = "\OML/cmm/m/it/10 ; rsq; \OT1/cmr/m/n/10 "$" [] Underfull \hbox (badness 10000) in paragraph at lines 3316--3321 []\OT1/cmr/m/n/10 legend('bottomright', leg-end = paste("$\OML/cmm/m/it/10 y \O T1/cmr/m/n/10 = [] Overfull \hbox (30.89163pt too wide) in paragraph at lines 3316--3321 \OT1/cmr/m/n/10 "\OML/cmm/m/it/10 ; round\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef \OT1/cmr/m/n/10 (\OML/cmm/m/it/10 model\OT1/cmr/m/n/10 )[2]\OML/cmm/m/it/10 ; \ OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[] x\OT1/cmr/m/n/10 +[]\OML/cmm/m/it/10 ; ro und\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 mode l\OT1/cmr/m/n/10 )[1]\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[]$ \OT1/cmr/m/n/10 ', [] (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--3328 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--3328 [] [47pdfTeX warning (ext4): destination with the same identifier (name{figure.11} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3331 ] Overfull \hbox (190.77408pt too wide) in paragraph at lines 3341--3344 []\OT1/cmr/m/n/10 <>= re-qu ire(tikzDevice) tikz('bareBonesExample.tex',width=4,height=4,bareBones=T) [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [48pdfTeX warning (ext4): destination with the same identifi er (name{figure.12}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3386 \end{tikzCodeBlock} ] Overfull \hbox (39.41106pt too wide) in paragraph at lines 3386--3386 [][] [] (./figs/bareBonesExample.tex) [49] Overfull \hbox (31.16272pt too wide) in paragraph at lines 3429--3430 \OT1/cmr/m/n/10 de-signed to be com-piled on its own. This means that in ad-di- tion to []\OT1/pcrs/m/n/10 \begin{tikzpicture} \OT1/cmr/m/n/10 and []\OT1/pcrs/ m/n/10 \end{tikzpicture} [] Overfull \hbox (90.55171pt too wide) in paragraph at lines 3431--3437 []\OT1/cmr/m/n/10 <>= re-q uire(tikzDevice) tikz('standAloneExample.tex',standAlone=T) [] Overfull \hbox (3.44038pt too wide) in paragraph at lines 3443--3446 []\OT1/cmr/m/n/10 catch <- sys-tem(paste(Sys.which('pdflatex'), '-interaction=b atchmode -output-directory figs/ figs/-s-tan-dAlone- [] ! You can't use `macro parameter character #' in vertical mode. l.3447 # If compiling the example failed, we don't want to include a broken... Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.3454 # %\Sexpr{print(pdfLink)} Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Underfull \hbox (badness 10000) in paragraph at lines 3447--3456 [] Underfull \hbox (badness 10000) in paragraph at lines 3447--3456 [] Overfull \hbox (9.08986pt too wide) in paragraph at lines 3457--3458 []\OT1/pcrs/m/n/10 \input{} \OT1/cmr/m/n/10 com-mand! Use []\OT1/pcrs/m/n/10 \i ncludegraphics{} \OT1/cmr/m/n/10 or load the [] pack-age and use []\OT1/pcrs/m/ n/10 \includepdf{}\OT1/cmr/m/n/10 . [] [50pdfTeX warning (ext4): destination with the same identifier (name{figure.13} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3462 ] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3483--3483 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41106pt too wide) in paragraph at lines 3560--3560 [][] [] [51] Underfull \vbox (badness 10000) detected at line 3560 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 3560--3560 [][] [] [52] Overfull \hbox (39.41106pt too wide) in paragraph at lines 3560--3560 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3566--3566 [][] [] LaTeX Warning: Reference `fig:xelatex' on page 53 undefined on input line 3568. File: img/testXeLaTeX.pdf Graphic file (type pdf) [53pdfTeX warning (ext4): destination with the same i dentifier (name{figure.14}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3576 \newpage ] LaTeX Warning: Reference `fig:annotation' on page 54 undefined on input line 35 79. ! Bad space factor (0). \@savsf l.3603 setTikzDefaults()\end{tikzCodeBlock} I allow only values in the range 1..32767 here. ! Extra \endgroup. \tikzCode@suspendOutputCapture ...phack \endgroup l.3603 setTikzDefaults()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (40.35718pt too wide) in paragraph at lines 3581--3603 []\OT1/cmr/m/n/10 <>= op-tions(ti kzLatexPackages = c(getOption('tikzLatexPackages'), [] Overfull \hbox (150.77412pt too wide) in paragraph at lines 3581--3603 \OT1/cmr/m/n/10 draw[decorate,very thick,red,", "dec-o-ra-tion=brace,amplitude= 20pt] (min) ", "-- node[single ar-row,anchor=tip,fill=white,left=20pt,draw=gree n] [] (./tikzDevice.lst) ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.3603 setTikzDefaults()\end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (36.66594pt too wide) in paragraph at lines 3603--3603 [][] [] ! LaTeX Error: \begin{document} ended by \end{tikzCodeBlock}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3603 setTikzDefaults()\end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.3603 setTikzDefaults()\end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. (./figs/annotation.tex) Overfull \hbox (24.06313pt too wide) in paragraph at lines 3615--3615 []\OT1/cmr/bx/n/14.4 The [] and [] Func-tions [] [54pdfTeX warning (ext4): destination with the same identifier (name{figure.15} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3620 ] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 3657--3657 [][] [] [55] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst Overfull \hbox (75.6459pt too wide) in paragraph at lines 117--119 [][][][][][][][][][][][] [] Overfull \hbox (216.04614pt too wide) in paragraph at lines 196--199 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (113.44597pt too wide) in paragraph at lines 222--224 [][][][][][][][][][][][][][] [] Overfull \hbox (950.44739pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (399.64645pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][] [] Overfull \hbox (178.24608pt too wide) in paragraph at lines 257--259 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[][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (3040.25093pt too wide) in paragraph at lines 270--272 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][] [] Overfull \hbox (1355.44807pt too wide) in paragraph at lines 274--276 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 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][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (853.24722pt too wide) in paragraph at lines 282--284 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][] [] Overfull \hbox (1328.44803pt too wide) in paragraph at lines 284--286 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][] [] Overfull \hbox (102.64595pt too wide) in paragraph at lines 299--301 [][][][][][][][][][][][] [] Overfull \hbox (442.84653pt too wide) in paragraph at lines 303--305 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (1933.24905pt too wide) in paragraph at lines 309--311 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (259.24622pt too wide) in paragraph at lines 327--329 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (91.84593pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (226.84616pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][] [] Overfull \hbox (523.84666pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][] [] Overfull \hbox (1112.44766pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (561.64673pt too wide) in paragraph at lines 368--370 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (145.84602pt too wide) in paragraph at lines 370--371 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) Underfull \vbox (badness 6461) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [56] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [57] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [58] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [59] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [60] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [61] Underfull \vbox (badness 10000) detected at line 4047 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4047--4047 [][] [] [62] Overfull \hbox (39.41106pt too wide) in paragraph at lines 4047--4047 [][] [] ! Too many }'s. l.4048 } You've closed more groups than you opened. Such booboos are generally harmless, so keep going. ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4049 \item[\code{tikzMetricsDictionary}] { When using the graphics device p... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4049 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [63] Overfull \hbox (39.41106pt too wide) in paragraph at lines 4053--4053 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4056 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass dec... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4056 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4060--4060 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4062 \item[\code{tikzFooter}] {A character vector. The footer to be used on... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4062 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4066--4066 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4068 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4068 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4076--4076 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4083--4083 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4086 \item[\code{tikzMetricPackages}] { A character vector. These are the e... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4086 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [64] Overfull \hbox (39.41106pt too wide) in paragraph at lines 4094--4094 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4097 \item[\code{tikzSanitizeCharacters}] {A character vector of special la... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4097 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4101--4101 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4103 \item[\code{tikzReplacementCharacters}] {A character vector of replace... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 4103 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4107--4107 [][] [] ! LaTeX Error: \begin{document} ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4109 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.4109 \end{description} Things are pretty mixed up, but I think the worst is over. LaTeX Warning: Reference `part:three' on page 65 undefined on input line 4113. Overfull \hbox (40.21104pt too wide) in paragraph at lines 4117--4117 [][] [] [65] LaTeX Warning: Reference `subsec:fontCalc' on page 66 undefined on input line 4 148. LaTeX Warning: Reference `sec:options' on page 66 undefined on input line 4153. LaTeX Warning: Reference `sec:options' on page 66 undefined on input line 4154. LaTeX Warning: Reference `sec:options' on page 66 undefined on input line 4155. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! [66] Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Overfull \hbox (45.69058pt too wide) in paragraph at lines 4212--4218 []\OT1/cmr/m/n/10 <>= re-quire(tikzDevice) tikz(' simpleEx.tex',width=3.5,height=3.5) plot(1,main='Hello [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 4245--4245 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--4251 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--4251 [] [67] Underfull \hbox (badness 10000) in paragraph at lines 4265--4269 []\OT1/cmr/m/n/10 <>= [] Underfull \hbox (badness 10000) in paragraph at lines 4265--4269 \OT1/cmr/m/n/10 re-quire(tikzDevice) tikz('latexEx.tex', [] ! Missing $ inserted. $ l.4276 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Underfull \hbox (badness 4416) in paragraph at lines 4273--4276 []\OT1/cmr/m/n/10 model <- lm(y x) rsq <- sum-mary( model [] Underfull \hbox (badness 7814) in paragraph at lines 4280--4282 []\OT1/cmr/m/n/10 mtext(paste("Linear model: $\OML/cmm/m/it/10 R[] \OT1/cmr/m/n /10 = "\OML/cmm/m/it/10 ; rsq; \OT1/cmr/m/n/10 "$" [] Underfull \hbox (badness 10000) in paragraph at lines 4283--4288 []\OT1/cmr/m/n/10 legend('bottomright', leg-end = paste("$\OML/cmm/m/it/10 y \O T1/cmr/m/n/10 = [] Overfull \hbox (30.89163pt too wide) in paragraph at lines 4283--4288 \OT1/cmr/m/n/10 "\OML/cmm/m/it/10 ; round\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef \OT1/cmr/m/n/10 (\OML/cmm/m/it/10 model\OT1/cmr/m/n/10 )[2]\OML/cmm/m/it/10 ; \ OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[] x\OT1/cmr/m/n/10 +[]\OML/cmm/m/it/10 ; ro und\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 mode l\OT1/cmr/m/n/10 )[1]\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[]$ \OT1/cmr/m/n/10 ', [] (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--4295 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--4295 [] [68pdfTeX warning (ext4): destination with the same identifier (name{figure.16} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.4298 ] Overfull \hbox (190.77408pt too wide) in paragraph at lines 4308--4311 []\OT1/cmr/m/n/10 <>= re-qu ire(tikzDevice) tikz('bareBonesExample.tex',width=4,height=4,bareBones=T) [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [69pdfTeX warning (ext4): destination with the same identifi er (name{figure.17}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.4353 \end{tikzCodeBlock} ] Overfull \hbox (39.41106pt too wide) in paragraph at lines 4353--4353 [][] [] (./figs/bareBonesExample.tex) [70] Overfull \hbox (31.16272pt too wide) in paragraph at lines 4396--4397 \OT1/cmr/m/n/10 de-signed to be com-piled on its own. This means that in ad-di- tion to []\OT1/pcrs/m/n/10 \begin{tikzpicture} \OT1/cmr/m/n/10 and []\OT1/pcrs/ m/n/10 \end{tikzpicture} [] Overfull \hbox (90.55171pt too wide) in paragraph at lines 4398--4404 []\OT1/cmr/m/n/10 <>= re-q uire(tikzDevice) tikz('standAloneExample.tex',standAlone=T) [] Overfull \hbox (3.44038pt too wide) in paragraph at lines 4410--4413 []\OT1/cmr/m/n/10 catch <- sys-tem(paste(Sys.which('pdflatex'), '-interaction=b atchmode -output-directory figs/ figs/-s-tan-dAlone- [] ! You can't use `macro parameter character #' in vertical mode. l.4414 # If compiling the example failed, we don't want to include a broken... Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.4421 # %\Sexpr{print(pdfLink)} Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Underfull \hbox (badness 10000) in paragraph at lines 4414--4423 [] Underfull \hbox (badness 10000) in paragraph at lines 4414--4423 [] Overfull \hbox (9.08986pt too wide) in paragraph at lines 4424--4425 []\OT1/pcrs/m/n/10 \input{} \OT1/cmr/m/n/10 com-mand! Use []\OT1/pcrs/m/n/10 \i ncludegraphics{} \OT1/cmr/m/n/10 or load the [] pack-age and use []\OT1/pcrs/m/ n/10 \includepdf{}\OT1/cmr/m/n/10 . [] [71pdfTeX warning (ext4): destination with the same identifier (name{figure.18} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.4429 ] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4450--4450 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41106pt too wide) in paragraph at lines 4527--4527 [][] [] [72] Underfull \vbox (badness 10000) detected at line 4527 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 4527--4527 [][] [] [73] Overfull \hbox (39.41106pt too wide) in paragraph at lines 4527--4527 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 4533--4533 [][] [] LaTeX Warning: Reference `fig:xelatex' on page 74 undefined on input line 4535. File: img/testXeLaTeX.pdf Graphic file (type pdf) [74pdfTeX warning (ext4): destination with the same i dentifier (name{figure.19}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.4543 \newpage ] LaTeX Warning: Reference `fig:annotation' on page 75 undefined on input line 45 46. Overfull \hbox (40.35718pt too wide) in paragraph at lines 4548--4553 []\OT1/cmr/m/n/10 <>= op-tions(ti kzLatexPackages = c(getOption('tikzLatexPackages'), [] Overfull \hbox (150.77412pt too wide) in paragraph at lines 4567--4571 \OT1/cmr/m/n/10 draw[decorate,very thick,red,", "dec-o-ra-tion=brace,amplitude= 20pt] (min) ", "-- node[single ar-row,anchor=tip,fill=white,left=20pt,draw=gree n] [] (./figs/annotation.tex) LaTeX Warning: `!h' float specifier changed to `!ht'. Overfull \hbox (32.16312pt too wide) in paragraph at lines 4594--4594 []\OT1/cmr/bx/n/14.4 The [] and [] Func-tions [] [75] [76pdfTeX warning (ext4): destination with the same identifier (name{figur e.20}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.4642 ] ! You can't use `macro parameter character #' in horizontal mode. l.4652 # Get metrics for 'y' Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Overfull \hbox (31.87088pt too wide) in paragraph at lines 4651--4655 []\OT1/cmr/m/n/10 <>= Get met-rics for 'y ' get-La-tex-Char-Met-rics(121) swe@veSt@rtOutput[1] [] ! You can't use `macro parameter character #' in vertical mode. l.4656 # Get metrics for 'x' - the second value is the descent Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.4657 # and should be zero or very close to zero. Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! Bad space factor (0). \@savsf l.4660 \end{tikzCodeBlock} I allow only values in the range 1..32767 here. ! Extra \endgroup. \tikzCode@suspendOutputCapture ...phack \endgroup l.4660 \end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. (./tikzDevice.lst) ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.4660 \end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (36.66594pt too wide) in paragraph at lines 4660--4660 [][] [] ! LaTeX Error: \begin{document} ended by \end{tikzCodeBlock}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4660 \end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.4660 \end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (55.86714pt too wide) in paragraph at lines 4662--4663 []\OT1/cmr/m/n/10 Note that char-ac-ters, along with num-bers out-side the rang e of [32-126], may not be passed to the [] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst Overfull \hbox (75.6459pt too wide) in paragraph at lines 117--119 [][][][][][][][][][][][] [] Overfull \hbox (216.04614pt too wide) in paragraph at lines 196--199 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (113.44597pt too wide) in paragraph at lines 222--224 [][][][][][][][][][][][][][] [] Overfull \hbox (950.44739pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (399.64645pt too wide) in paragraph at lines 243--245 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][] [] Overfull \hbox (178.24608pt too wide) in paragraph at lines 257--259 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[][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][] [] Overfull \hbox (3040.25093pt too wide) in paragraph at lines 270--272 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][] [] Overfull \hbox (1355.44807pt too wide) in paragraph at lines 274--276 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 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][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (853.24722pt too wide) in paragraph at lines 282--284 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][] [] Overfull \hbox (1328.44803pt too wide) in paragraph at lines 284--286 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][] [] Overfull \hbox (102.64595pt too wide) in paragraph at lines 299--301 [][][][][][][][][][][][] [] Overfull \hbox (442.84653pt too wide) in paragraph at lines 303--305 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (1933.24905pt too wide) in paragraph at lines 309--311 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (259.24622pt too wide) in paragraph at lines 327--329 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][] [] Overfull \hbox (91.84593pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][] [] Overfull \hbox (226.84616pt too wide) in paragraph at lines 348--351 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][] [] Overfull \hbox (523.84666pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][] [] Overfull \hbox (1112.44766pt too wide) in paragraph at lines 352--355 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (561.64673pt too wide) in paragraph at lines 368--370 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][ ][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (145.84602pt too wide) in paragraph at lines 370--371 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [77] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [78] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [79] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [80] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [81] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [82] Underfull \vbox (badness 10000) detected at line 5036 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5036--5036 [][] [] [83] Overfull \hbox (39.41106pt too wide) in paragraph at lines 5036--5036 [][] [] ! Too many }'s. l.5037 } You've closed more groups than you opened. Such booboos are generally harmless, so keep going. ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5038 \item[\code{tikzMetricsDictionary}] { When using the graphics device p... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5038 [][] [] [84] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5042--5042 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5045 \item[\code{tikzDocumentDeclaration}] {A string. The documentclass dec... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5045 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5049--5049 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5051 \item[\code{tikzFooter}] {A character vector. The footer to be used on... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5051 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5055--5055 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5057 \item[\code{tikzLatexPackages}] { A character vector. These are the pa... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5057 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5065--5065 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5072--5072 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5075 \item[\code{tikzMetricPackages}] { A character vector. These are the e... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5075 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [85] Overfull \hbox (39.41106pt too wide) in paragraph at lines 5083--5083 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5086 \item[\code{tikzSanitizeCharacters}] {A character vector of special la... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5086 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5090--5090 [][] [] ! LaTeX Error: Lonely \item--perhaps a missing list environment. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5092 \item[\code{tikzReplacementCharacters}] {A character vector of replace... Try typing to proceed. If that doesn't work, type X to quit. Underfull \hbox (badness 10000) detected at line 5092 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5096--5096 [][] [] ! LaTeX Error: \begin{document} ended by \end{description}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5098 \end{description} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.5098 \end{description} Things are pretty mixed up, but I think the worst is over. LaTeX Warning: Reference `part:three' on page 86 undefined on input line 5102. Overfull \hbox (40.21104pt too wide) in paragraph at lines 5106--5106 [][] [] [86] LaTeX Warning: Reference `subsec:fontCalc' on page 87 undefined on input line 5 137. LaTeX Warning: Reference `sec:options' on page 87 undefined on input line 5142. LaTeX Warning: Reference `sec:options' on page 87 undefined on input line 5143. LaTeX Warning: Reference `sec:options' on page 87 undefined on input line 5144. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! [87] Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! Overfull \hbox (45.69058pt too wide) in paragraph at lines 5201--5207 []\OT1/cmr/m/n/10 <>= re-quire(tikzDevice) tikz(' simpleEx.tex',width=3.5,height=3.5) plot(1,main='Hello [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41107pt too wide) in paragraph at lines 5234--5234 [][] [] (./figs/simpleEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 93--5240 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 93--5240 [] [88] Underfull \hbox (badness 10000) in paragraph at lines 5254--5258 []\OT1/cmr/m/n/10 <>= [] Underfull \hbox (badness 10000) in paragraph at lines 5254--5258 \OT1/cmr/m/n/10 re-quire(tikzDevice) tikz('latexEx.tex', [] ! Missing $ inserted. $ l.5265 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Underfull \hbox (badness 4416) in paragraph at lines 5262--5265 []\OT1/cmr/m/n/10 model <- lm(y x) rsq <- sum-mary( model [] Underfull \hbox (badness 7814) in paragraph at lines 5269--5271 []\OT1/cmr/m/n/10 mtext(paste("Linear model: $\OML/cmm/m/it/10 R[] \OT1/cmr/m/n /10 = "\OML/cmm/m/it/10 ; rsq; \OT1/cmr/m/n/10 "$" [] Underfull \hbox (badness 10000) in paragraph at lines 5272--5277 []\OT1/cmr/m/n/10 legend('bottomright', leg-end = paste("$\OML/cmm/m/it/10 y \O T1/cmr/m/n/10 = [] Overfull \hbox (30.89163pt too wide) in paragraph at lines 5272--5277 \OT1/cmr/m/n/10 "\OML/cmm/m/it/10 ; round\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef \OT1/cmr/m/n/10 (\OML/cmm/m/it/10 model\OT1/cmr/m/n/10 )[2]\OML/cmm/m/it/10 ; \ OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[] x\OT1/cmr/m/n/10 +[]\OML/cmm/m/it/10 ; ro und\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 coef\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 mode l\OT1/cmr/m/n/10 )[1]\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 3)\OML/cmm/m/it/10 ;[]$ \OT1/cmr/m/n/10 ', [] (./figs/latexEx.tex) Overfull \hbox (41.95168pt too wide) in paragraph at lines 138--5284 [][] [] Underfull \hbox (badness 10000) in paragraph at lines 138--5284 [] [89pdfTeX warning (ext4): destination with the same identifier (name{figure.21} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.5287 ] Overfull \hbox (190.77408pt too wide) in paragraph at lines 5297--5300 []\OT1/cmr/m/n/10 <>= re-qu ire(tikzDevice) tikz('bareBonesExample.tex',width=4,height=4,bareBones=T) [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [90pdfTeX warning (ext4): destination with the same identifi er (name{figure.22}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.5342 \end{tikzCodeBlock} ] Overfull \hbox (39.41106pt too wide) in paragraph at lines 5342--5342 [][] [] (./figs/bareBonesExample.tex) [91] Overfull \hbox (31.16272pt too wide) in paragraph at lines 5385--5386 \OT1/cmr/m/n/10 de-signed to be com-piled on its own. This means that in ad-di- tion to []\OT1/pcrs/m/n/10 \begin{tikzpicture} \OT1/cmr/m/n/10 and []\OT1/pcrs/ m/n/10 \end{tikzpicture} [] Overfull \hbox (90.55171pt too wide) in paragraph at lines 5387--5393 []\OT1/cmr/m/n/10 <>= re-q uire(tikzDevice) tikz('standAloneExample.tex',standAlone=T) [] Overfull \hbox (3.44038pt too wide) in paragraph at lines 5399--5402 []\OT1/cmr/m/n/10 catch <- sys-tem(paste(Sys.which('pdflatex'), '-interaction=b atchmode -output-directory figs/ figs/-s-tan-dAlone- [] ! You can't use `macro parameter character #' in vertical mode. l.5403 # If compiling the example failed, we don't want to include a broken... Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.5410 # %\Sexpr{print(pdfLink)} Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Underfull \hbox (badness 10000) in paragraph at lines 5403--5412 [] Underfull \hbox (badness 10000) in paragraph at lines 5403--5412 [] Overfull \hbox (9.08986pt too wide) in paragraph at lines 5413--5414 []\OT1/pcrs/m/n/10 \input{} \OT1/cmr/m/n/10 com-mand! Use []\OT1/pcrs/m/n/10 \i ncludegraphics{} \OT1/cmr/m/n/10 or load the [] pack-age and use []\OT1/pcrs/m/ n/10 \includepdf{}\OT1/cmr/m/n/10 . [] [92pdfTeX warning (ext4): destination with the same identifier (name{figure.23} ) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.5418 ] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5439--5439 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (9.41106pt too wide) in paragraph at lines 5516--5516 [][] [] [93] Underfull \vbox (badness 10000) detected at line 5516 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 5516--5516 [][] [] [94] Overfull \hbox (39.41106pt too wide) in paragraph at lines 5516--5516 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5522--5522 [][] [] LaTeX Warning: Reference `fig:xelatex' on page 95 undefined on input line 5524. File: img/testXeLaTeX.pdf Graphic file (type pdf) [95pdfTeX warning (ext4): destination with the same i dentifier (name{figure.24}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.5532 \newpage ] LaTeX Warning: Reference `fig:annotation' on page 96 undefined on input line 55 35. Overfull \hbox (40.35718pt too wide) in paragraph at lines 5537--5542 []\OT1/cmr/m/n/10 <>= op-tions(ti kzLatexPackages = c(getOption('tikzLatexPackages'), [] Overfull \hbox (150.77412pt too wide) in paragraph at lines 5556--5560 \OT1/cmr/m/n/10 draw[decorate,very thick,red,", "dec-o-ra-tion=brace,amplitude= 20pt] (min) ", "-- node[single ar-row,anchor=tip,fill=white,left=20pt,draw=gree n] [] (./figs/annotation.tex) LaTeX Warning: `!h' float specifier changed to `!ht'. Overfull \hbox (32.16312pt too wide) in paragraph at lines 5583--5583 []\OT1/cmr/bx/n/14.4 The [] and [] Func-tions [] [96] [97pdfTeX warning (ext4): destination with the same identifier (name{figur e.25}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.5631 ] ! You can't use `macro parameter character #' in horizontal mode. l.5641 # Get metrics for 'y' Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in vertical mode. l.5644 # Get metrics for 'x' - the second value is the descent Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.5645 # and should be zero or very close to zero. Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Overfull \hbox (55.86714pt too wide) in paragraph at lines 5649--5650 []\OT1/cmr/m/n/10 Note that char-ac-ters, along with num-bers out-side the rang e of [32-126], may not be passed to the [] [] Overfull \hbox (77.57932pt too wide) in paragraph at lines 5651--5654 []\OT1/cmr/m/n/10 <>= get-La-tex-Char-Me t-rics('y') swe@veSt@rtOutputNULLswe@veEndOutput [] ! You can't use `macro parameter character #' in vertical mode. l.5658 # Will return metrics for 'y' Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! Bad space factor (0). \@savsf l.5661 \end{tikzCodeBlock} I allow only values in the range 1..32767 here. ! Extra \endgroup. \tikzCode@suspendOutputCapture ...phack \endgroup l.5661 \end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. Overfull \hbox (90.10724pt too wide) in paragraph at lines 5658--5661 []\OT1/cmr/m/n/10 Will re-turn met-rics for 'y' get-La-tex-Char-Met-rics(121.99 ) swe@veSt@rtOutput[1] 4.30450 1.94397 5.27649swe@veEndOutput [] (./tikzDevice.lst) ! Package pgfkeys Error: I do not know the key '/tikzCode/code body' and I am g oing to ignore it. Perhaps you misspelled it. See the pgfkeys package documentation for explanation. Type H for immediate help. ... l.5661 \end{tikzCodeBlock} (That was another \errmessage.) Overfull \hbox (36.66594pt too wide) in paragraph at lines 5661--5661 [][] [] ! LaTeX Error: \begin{document} ended by \end{tikzCodeBlock}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.5661 \end{tikzCodeBlock} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Extra \endgroup. \endgroup l.5661 \end{tikzCodeBlock} Things are pretty mixed up, but I think the worst is over. [98] LaTeX Warning: Reference `tikz:required' on page 99 undefined on input line 567 4. [99] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5708--5708 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5714--5714 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5726--5726 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [100] Overfull \hbox (39.41106pt too wide) in paragraph at lines 5730--5730 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5737--5737 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5748--5748 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5763--5763 [][] [] [101] Overfull \hbox (40.21104pt too wide) in paragraph at lines 5780--5780 [] [] [102] \yone=\dimen180 \ytwo=\dimen181 \yone=\dimen182 \ytwo=\dimen183 \xone=\dimen184 \xtwo=\dimen185 [103] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 5962--5962 [][] [] [104] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6000--6000 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Underfull \vbox (badness 10000) detected at line 6021 [] Overfull \hbox (9.41106pt too wide) in paragraph at lines 6021--6021 [][] [] [105] Overfull \hbox (39.41106pt too wide) in paragraph at lines 6021--6021 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6033--6033 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6040--6040 [][] [] [106] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6052--6052 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6071--6071 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [107] Overfull \hbox (39.41106pt too wide) in paragraph at lines 6086--6086 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6110--6110 [][] [] [108] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6116--6116 [][] [] LaTeX Font Info: Font shape `OT1/pcrs/m/n' will be (Font) scaled to size 8.09995pt on input line 6131. \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6145--6145 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6151--6151 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) [109] Overfull \hbox (39.41106pt too wide) in paragraph at lines 6157--6157 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6163--6163 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6169--6169 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6179--6179 [][] [] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6194--6194 [][] [] [110] \openout4 = `tikzDevice.lst'. (./tikzDevice.lst) Overfull \hbox (39.41106pt too wide) in paragraph at lines 6209--6209 [][] [] Overfull \hbox (10.72285pt too wide) in paragraph at lines 6216--6216 []\OT1/cmr/bx/n/14.4 On the Im-por-tance of Font and Style Con-sis-tency in Re- ports [] Overfull \hbox (0.50278pt too wide) in paragraph at lines 6219--6219 []\OT1/cmr/bx/n/14.4 The pgf-Sweave Pack-age and Au-to-matic Re-port Gen-er-a-t ion [] [111] No file tikzDevice.bbl. Package natbib Warning: There were undefined citations. (./tikzDevice.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) Here is how much of TeX's memory you used: 22021 strings out of 494781 368271 string characters out of 1177155 1339388 words of memory out of 3000000 21808 multiletter control sequences out of 15000+50000 19207 words of font info for 65 fonts, out of 3000000 for 9000 212 hyphenation exceptions out of 8191 50i,14n,78p,1080b,2367s stack positions out of 5000i,500n,10000p,200000b,50000s {/usr/share/texmf/fonts/enc/dvips/cm-super/cm-super-t1.enc}{/usr/share/texmf- texlive/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/ cm-super-ts1.enc}< /usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmsy6.pfb>< /usr/share/texmf-texlive/fonts/type1/urw/courier/ucrb8a.pfb> Output written on tikzDevice.pdf (113 pages, 1183904 bytes). PDF statistics: 3855 PDF objects out of 4296 (max. 8388607) 2732 named destinations out of 2984 (max. 500000) 23 words of extra memory for PDF output out of 10000 (max. 10000000)