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Version: 1.15.20
Result: OK
Check time: 2017-04-21 22:46

Distribution log

--- running R CMD build for knitr (project knitr)
* checking for file 'knitr/DESCRIPTION' ... OK
* preparing 'knitr':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ......
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
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Babel <3.9l> and hyphenation patterns for 2 languages loaded.
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[]\T1/ptm/m/n/10 Full doc-u-men-ta-tion and de-mos: [][]$\T1/zi4/m/n/10 http :
/ / yihui . name / knitr/$[][]\T1/ptm/m/n/10 ; FAQ's: [][]$\T1/zi4/m/n/10 http
: / / bit . ly / knitr-[]faq$[][]
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\T1/ptm/m/n/10 you gen-er-ate \T1/zi4/m/n/10 raw_output() \T1/ptm/m/n/10 to the
Mark-down out-put. In the pre-processor, you can \T1/zi4/m/n/10 extract_raw_ou
tput()
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 my-figure/\T1/ptm/m/n/10 ', you are not rec-om-m
ended to use hard-coded fig-ure paths like `\T1/zi4/m/n/10 \includegraphics{my-
figure/foo-1.pdf}\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 stead, you should use `\T1/zi4/m/n/10 \Sexpr{fig_chunk(\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )}\T1/ptm/m/n/10 ' or `\T1/zi4/
m/n/10 ![](\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r fig_chunk(\TS1/zi4/m/n/10 '\T1/zi4
/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pn
g\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 )\T1/ptm/m/n/
10 '.
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[]\T1/ptm/m/n/10 These hooks are mainly for the pack-age op-tion \T1/zi4/m/n/10
animation.fun\T1/ptm/m/n/10 , e.g. you can set \T1/zi4/m/n/10 opts_knit$set(an
imation.fun = hook_scianimator)\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Depending on the op-tions passed over, \T1/zi4/m/n/10 hook_plo
t_tex \T1/ptm/m/n/10 may re-turn the nor-mal `\T1/zi4/m/n/10 \includegraphics{}
\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 many other op-tions into con-sid-er-a-tion to align plots and se
t fig-ure sizes, etc. Sim-i-larly, \T1/zi4/m/n/10 hook_plot_html\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 cal im-age files to Imgur, e.g. set the pack-age op-tion \T1/zi4
/m/n/10 opts_knit$set(upload.fun = imgur_upload)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 you want to write `\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r 1+1\TS1/zi4
/m/n/10 `\T1/ptm/m/n/10 ' lit-er-ally in an R Mark-down doc-u-ment, you may wri
te `\TS1/zi4/m/n/10 `` `\T1/zi4/m/n/10 r knitr::inline_expr(\TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 1+1\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `
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[]\T1/zi4/m/n/10 kable(x, format, digits = getOption("digits"), row.names = NA
, col.names = NA, align,[]
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[]\T1/ptm/m/n/10 a list of ar-gu-ments to be passed to [][]\T1/zi4/m/n/10 forma
t[][][]() \T1/ptm/m/n/10 to for-mat ta-ble val-ues, e.g. \T1/zi4/m/n/10 list(bi
g.mark = \TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )

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[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 https : / / github . com / yihui / kni
tr-[]examples / blob / master / 091-[]knitr-[]table . Rnw$[][] \T1/ptm/m/n/10 f
or some
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[]\T1/ptm/m/n/10 The ar-gu-ments \T1/zi4/m/n/10 input \T1/ptm/m/n/10 and \T1/zi
4/m/n/10 output \T1/ptm/m/n/10 do not have to be re-stricted to files; they can
be \T1/zi4/m/n/10 stdin()\T1/ptm/m/n/10 /\T1/zi4/m/n/10 stdout()
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[]\T1/zi4/m/n/10 knit2html(input, output = NULL, ..., envir = parent.frame(),
text = NULL, quiet = FALSE,[]
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[]\T1/zi4/m/n/10 knit2pdf(input, output = NULL, compiler = NULL, envir = paren
t.frame(), quiet = FALSE,[]
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[]\T1/ptm/m/n/10 a log-i-cal vec-tor of length 2: whether to use the short-code
`\T1/zi4/m/n/10 [sourcecode lang=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 lang\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 ]\T1/ptm/m/n/10 '
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[]\T1/ptm/m/n/10 The en-gine func-tion has one ar-gu-ment \T1/zi4/m/n/10 option
s\T1/ptm/m/n/10 : the source code of the cur-rent chunk is in \T1/zi4/m/n/10 op
tions$code\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 case we can pass it through the \T1/zi4/m/n/10 engine.path \T1/p
tm/m/n/10 op-tion. For ex-am-ple, \T1/zi4/m/n/10 engine=\TS1/zi4/m/n/10 '\T1/zi
4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.path=\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 /usr/bin/ruby1.9.1\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 Ad-di-tional com-mand line ar-gu-ments can be passed through \T1
/zi4/m/n/10 options$engine.opts\T1/ptm/m/n/10 , e.g. \T1/zi4/m/n/10 engine=\TS1
/zi4/m/n/10 '\T1/zi4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.opts=\T
S1/zi4/m/n/10 '\T1/zi4/m/n/10 -v\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Usage: [][]$\T1/zi4/m/n/10 http : / / yihui . name / knitr / o
bjects$[][]\T1/ptm/m/n/10 ; ex-am-ples: [][]$\T1/zi4/m/n/10 http : / / yihui .
name / knitr / demo / engines/$[][]
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[]\T1/zi4/m/n/10 knit_expand(file, ..., text = readLines(file, warn = FALSE),
delim = c("{{", "}}"))[]
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[]\T1/ptm/m/n/10 It re-turns the \T1/zi4/m/n/10 envir \T1/ptm/m/n/10 ar-gu-ment
of [][]\T1/zi4/m/n/10 knit[][][]\T1/ptm/m/n/10 , e.g. if we call [][]\T1/zi4/m
/n/10 knit[][][]() \T1/ptm/m/n/10 in the global en-vi-ron-ment, \T1/zi4/m/n/10
knit_global()
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[]\T1/ptm/m/n/10 It is rec-om-mended to leave a \T1/zi4/m/n/10 ... \T1/ptm/m/n/
10 ar-gu-ment in your method, to al-low fu-ture changes of the \T1/zi4/m/n/10 k
nit_print()
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[]\T1/ptm/m/n/10 the path of the cache database (nor-mally set in the global ch
unk op-tion \T1/zi4/m/n/10 cache.path\T1/ptm/m/n/10 )

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[]\T1/ptm/m/n/10 whether to [][]\T1/zi4/m/n/10 lazyLoad[][][] \T1/ptm/m/n/10 th
e cache database (de-pend-ing on the chunk op-tion \T1/zi4/m/n/10 cache.lazy =
TRUE
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[]\T1/ptm/m/n/10 Normally we set up the global op-tions once in the first code
chunk in a doc-u-ment us-ing \T1/zi4/m/n/10 opts_chunk$set()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 PDFCrop: [][]$\T1/zi4/m/n/10 https : / / www . ctan . org / pk
g / pdfcrop$[][]\T1/ptm/m/n/10 ; the \T1/zi4/m/n/10 convert \T1/ptm/m/n/10 com-
mand in Im-ageMag-ick: [][]$\T1/zi4/m/n/10 http :
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[]\T1/zi4/m/n/10 read_chunk(path, lines = readLines(path, warn = FALSE), label
s = NULL, from = NULL,[]
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[]\T1/ptm/m/n/10 Yihui Xie; the idea of the sec-ond ap-proach came from Pe-ter
Ruck-de-schel (au-thor of the \T1/ptm/b/n/10 SweaveListingUtils
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[]\T1/ptm/m/n/10 There are three vari-ants of mark-down doc-u-ments: or-di-nary
mark-down (\T1/zi4/m/n/10 render_markdown(strict = TRUE)\T1/ptm/m/n/10 ),

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\T1/ptm/m/n/10 ex-tended mark-down (e.g. GitHub Fla-vored Mark-down and pan-doc
; \T1/zi4/m/n/10 render_markdown(strict = FALSE)\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 Jekyll and Liq-uid: [][]$\T1/zi4/m/n/10 https : / / github . c
om / jekyll / jekyll / wiki / Liquid-[]Extensions$[][]\T1/ptm/m/n/10 ; pret-tif
y.js:
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[]\T1/zi4/m/n/10 stitch(script, template = system.file("misc", "knitr-template
.Rnw", package = "knitr"),[]
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[]\T1/ptm/m/n/10 The pseudo com-mand `\T1/zi4/m/n/10 \SweaveInput{file.Rnw}\T1/
ptm/m/n/10 ' is con-verted to a code chunk header \T1/zi4/m/n/10 < i4/m/n/10 '\T1/zi4/m/n/10 file.Rnw\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 >>=\T1/ptm/m/
n/10 .

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[]\T1/ptm/m/n/10 Similarly `\T1/zi4/m/n/10 \SweaveOpts{opt = value}\T1/ptm/m/n/
10 ' is con-verted to a code chunk `\T1/zi4/m/n/10 opts_chunk$set(opt = value)\
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\T1/ptm/m/n/10 mat-i-cally gen-er-ated); \T1/zi4/m/n/10 fig=FALSE \T1/ptm/m/n/1
0 is changed to \T1/zi4/m/n/10 fig.keep=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 none\TS
1/zi4/m/n/10 '\T1/ptm/m/n/10 ; the de-vices \T1/zi4/m/n/10 pdf/jpeg/png/eps/tik
z=TRUE

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\T1/ptm/m/n/10 are con-verted to \T1/zi4/m/n/10 dev=\TS1/zi4/m/n/10 '\T1/zi4/m/
n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 jpeg\T
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10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 postscript\TS1/zi4/m/n/10 '
\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 tikz\TS1/zi4/m/n/10 '\T1/ptm/m/
n/10 ; \T1/zi4/m/n/10 pdf/jpeg/png/eps/tikz=FALSE
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 Suggests\T1/ptm/m/n/10 ' field of your `\T1/zi4/
m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file. Also make sure the ex-e-cuta-bles \T1/
zi4/m/n/10 pandoc \T1/ptm/m/n/10 and \T1/zi4/m/n/10 pandoc-citeproc

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\T1/zi4/m/n/10 which pandoc-citeproc \T1/ptm/m/n/10 in the ter-mi-nal (or \T1/z
i4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pandoc\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 ) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 pandoc-citeproc\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )
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[]\T1/ptm/m/n/10 a pre-fix string for keys in Bib-TeX en-tries; by de-fault, it
is `\T1/zi4/m/n/10 R-\T1/ptm/m/n/10 ' un-less [][]\T1/zi4/m/n/10 option[][][](
\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 knitr.bib.prefix\TS1/zi4/m/n/10 '\T1/zi4/m/n/10
)

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[]\T1/ptm/m/n/10 The ci-ta-tion is forced to be gen-er-ated from the `\T1/zi4/m
/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file of the pack-age (\T1/zi4/m/n/10 citation
(auto = TRUE)\T1/ptm/m/n/10 ).
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[]\T1/ptm/m/n/10 Full doc-u-men-ta-tion and de-mos: [][]$\T1/zi4/m/n/10 http :
/ / yihui . name / knitr/$[][]\T1/ptm/m/n/10 ; FAQ's: [][]$\T1/zi4/m/n/10 http
: / / bit . ly / knitr-[]faq$[][]
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\T1/ptm/m/n/10 you gen-er-ate \T1/zi4/m/n/10 raw_output() \T1/ptm/m/n/10 to the
Mark-down out-put. In the pre-processor, you can \T1/zi4/m/n/10 extract_raw_ou
tput()
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 my-figure/\T1/ptm/m/n/10 ', you are not rec-om-m
ended to use hard-coded fig-ure paths like `\T1/zi4/m/n/10 \includegraphics{my-
figure/foo-1.pdf}\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 stead, you should use `\T1/zi4/m/n/10 \Sexpr{fig_chunk(\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )}\T1/ptm/m/n/10 ' or `\T1/zi4/
m/n/10 ![](\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r fig_chunk(\TS1/zi4/m/n/10 '\T1/zi4
/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pn
g\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 )\T1/ptm/m/n/
10 '.
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[]\T1/ptm/m/n/10 These hooks are mainly for the pack-age op-tion \T1/zi4/m/n/10
animation.fun\T1/ptm/m/n/10 , e.g. you can set \T1/zi4/m/n/10 opts_knit$set(an
imation.fun = hook_scianimator)\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Depending on the op-tions passed over, \T1/zi4/m/n/10 hook_plo
t_tex \T1/ptm/m/n/10 may re-turn the nor-mal `\T1/zi4/m/n/10 \includegraphics{}
\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 many other op-tions into con-sid-er-a-tion to align plots and se
t fig-ure sizes, etc. Sim-i-larly, \T1/zi4/m/n/10 hook_plot_html\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 cal im-age files to Imgur, e.g. set the pack-age op-tion \T1/zi4
/m/n/10 opts_knit$set(upload.fun = imgur_upload)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 you want to write `\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r 1+1\TS1/zi4
/m/n/10 `\T1/ptm/m/n/10 ' lit-er-ally in an R Mark-down doc-u-ment, you may wri
te `\TS1/zi4/m/n/10 `` `\T1/zi4/m/n/10 r knitr::inline_expr(\TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 1+1\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `
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[]\T1/zi4/m/n/10 kable(x, format, digits = getOption("digits"), row.names = NA
, col.names = NA, align,[]

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[]\T1/ptm/m/n/10 a list of ar-gu-ments to be passed to [][]\T1/zi4/m/n/10 forma
t[][][]() \T1/ptm/m/n/10 to for-mat ta-ble val-ues, e.g. \T1/zi4/m/n/10 list(bi
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[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 https : / / github . com / yihui / kni
tr-[]examples / blob / master / 091-[]knitr-[]table . Rnw$[][] \T1/ptm/m/n/10 f
or some
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[]\T1/ptm/m/n/10 The ar-gu-ments \T1/zi4/m/n/10 input \T1/ptm/m/n/10 and \T1/zi
4/m/n/10 output \T1/ptm/m/n/10 do not have to be re-stricted to files; they can
be \T1/zi4/m/n/10 stdin()\T1/ptm/m/n/10 /\T1/zi4/m/n/10 stdout()
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[]\T1/zi4/m/n/10 knit2html(input, output = NULL, ..., envir = parent.frame(),
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[]\T1/zi4/m/n/10 knit2pdf(input, output = NULL, compiler = NULL, envir = paren
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[]\T1/ptm/m/n/10 a log-i-cal vec-tor of length 2: whether to use the short-code
`\T1/zi4/m/n/10 [sourcecode lang=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 lang\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 ]\T1/ptm/m/n/10 '
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[]\T1/ptm/m/n/10 The en-gine func-tion has one ar-gu-ment \T1/zi4/m/n/10 option
s\T1/ptm/m/n/10 : the source code of the cur-rent chunk is in \T1/zi4/m/n/10 op
tions$code\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 case we can pass it through the \T1/zi4/m/n/10 engine.path \T1/p
tm/m/n/10 op-tion. For ex-am-ple, \T1/zi4/m/n/10 engine=\TS1/zi4/m/n/10 '\T1/zi
4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.path=\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 /usr/bin/ruby1.9.1\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 Ad-di-tional com-mand line ar-gu-ments can be passed through \T1
/zi4/m/n/10 options$engine.opts\T1/ptm/m/n/10 , e.g. \T1/zi4/m/n/10 engine=\TS1
/zi4/m/n/10 '\T1/zi4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.opts=\T
S1/zi4/m/n/10 '\T1/zi4/m/n/10 -v\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .
[33]
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[]\T1/ptm/m/n/10 Usage: [][]$\T1/zi4/m/n/10 http : / / yihui . name / knitr / o
bjects$[][]\T1/ptm/m/n/10 ; ex-am-ples: [][]$\T1/zi4/m/n/10 http : / / yihui .
name / knitr / demo / engines/$[][]
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[]\T1/zi4/m/n/10 knit_expand(file, ..., text = readLines(file, warn = FALSE),
delim = c("{{", "}}"))[]
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[]\T1/ptm/m/n/10 It re-turns the \T1/zi4/m/n/10 envir \T1/ptm/m/n/10 ar-gu-ment
of [][]\T1/zi4/m/n/10 knit[][][]\T1/ptm/m/n/10 , e.g. if we call [][]\T1/zi4/m
/n/10 knit[][][]() \T1/ptm/m/n/10 in the global en-vi-ron-ment, \T1/zi4/m/n/10
knit_global()
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[]\T1/ptm/m/n/10 It is rec-om-mended to leave a \T1/zi4/m/n/10 ... \T1/ptm/m/n/
10 ar-gu-ment in your method, to al-low fu-ture changes of the \T1/zi4/m/n/10 k
nit_print()
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[]\T1/ptm/m/n/10 the path of the cache database (nor-mally set in the global ch
unk op-tion \T1/zi4/m/n/10 cache.path\T1/ptm/m/n/10 )

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[]\T1/ptm/m/n/10 whether to [][]\T1/zi4/m/n/10 lazyLoad[][][] \T1/ptm/m/n/10 th
e cache database (de-pend-ing on the chunk op-tion \T1/zi4/m/n/10 cache.lazy =
TRUE
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[]\T1/ptm/m/n/10 Normally we set up the global op-tions once in the first code
chunk in a doc-u-ment us-ing \T1/zi4/m/n/10 opts_chunk$set()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 PDFCrop: [][]$\T1/zi4/m/n/10 https : / / www . ctan . org / pk
g / pdfcrop$[][]\T1/ptm/m/n/10 ; the \T1/zi4/m/n/10 convert \T1/ptm/m/n/10 com-
mand in Im-ageMag-ick: [][]$\T1/zi4/m/n/10 http :
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[]\T1/zi4/m/n/10 read_chunk(path, lines = readLines(path, warn = FALSE), label
s = NULL, from = NULL,[]
[55]
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[]\T1/ptm/m/n/10 Yihui Xie; the idea of the sec-ond ap-proach came from Pe-ter
Ruck-de-schel (au-thor of the \T1/ptm/b/n/10 SweaveListingUtils
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[]\T1/ptm/m/n/10 There are three vari-ants of mark-down doc-u-ments: or-di-nary
mark-down (\T1/zi4/m/n/10 render_markdown(strict = TRUE)\T1/ptm/m/n/10 ),

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\T1/ptm/m/n/10 ex-tended mark-down (e.g. GitHub Fla-vored Mark-down and pan-doc
; \T1/zi4/m/n/10 render_markdown(strict = FALSE)\T1/ptm/m/n/10 ),
[58]
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[]\T1/ptm/m/n/10 Jekyll and Liq-uid: [][]$\T1/zi4/m/n/10 https : / / github . c
om / jekyll / jekyll / wiki / Liquid-[]Extensions$[][]\T1/ptm/m/n/10 ; pret-tif
y.js:
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[]\T1/zi4/m/n/10 stitch(script, template = system.file("misc", "knitr-template
.Rnw", package = "knitr"),[]
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[]\T1/ptm/m/n/10 The pseudo com-mand `\T1/zi4/m/n/10 \SweaveInput{file.Rnw}\T1/
ptm/m/n/10 ' is con-verted to a code chunk header \T1/zi4/m/n/10 < i4/m/n/10 '\T1/zi4/m/n/10 file.Rnw\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 >>=\T1/ptm/m/
n/10 .

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[]\T1/ptm/m/n/10 Similarly `\T1/zi4/m/n/10 \SweaveOpts{opt = value}\T1/ptm/m/n/
10 ' is con-verted to a code chunk `\T1/zi4/m/n/10 opts_chunk$set(opt = value)\
T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 mat-i-cally gen-er-ated); \T1/zi4/m/n/10 fig=FALSE \T1/ptm/m/n/1
0 is changed to \T1/zi4/m/n/10 fig.keep=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 none\TS
1/zi4/m/n/10 '\T1/ptm/m/n/10 ; the de-vices \T1/zi4/m/n/10 pdf/jpeg/png/eps/tik
z=TRUE

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\T1/ptm/m/n/10 are con-verted to \T1/zi4/m/n/10 dev=\TS1/zi4/m/n/10 '\T1/zi4/m/
n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 jpeg\T
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10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 postscript\TS1/zi4/m/n/10 '
\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 tikz\TS1/zi4/m/n/10 '\T1/ptm/m/
n/10 ; \T1/zi4/m/n/10 pdf/jpeg/png/eps/tikz=FALSE
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 Suggests\T1/ptm/m/n/10 ' field of your `\T1/zi4/
m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file. Also make sure the ex-e-cuta-bles \T1/
zi4/m/n/10 pandoc \T1/ptm/m/n/10 and \T1/zi4/m/n/10 pandoc-citeproc

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\T1/zi4/m/n/10 which pandoc-citeproc \T1/ptm/m/n/10 in the ter-mi-nal (or \T1/z
i4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pandoc\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 ) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 pandoc-citeproc\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )
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[]\T1/ptm/m/n/10 a pre-fix string for keys in Bib-TeX en-tries; by de-fault, it
is `\T1/zi4/m/n/10 R-\T1/ptm/m/n/10 ' un-less [][]\T1/zi4/m/n/10 option[][][](
\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 knitr.bib.prefix\TS1/zi4/m/n/10 '\T1/zi4/m/n/10
)

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[]\T1/ptm/m/n/10 The ci-ta-tion is forced to be gen-er-ated from the `\T1/zi4/m
/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file of the pack-age (\T1/zi4/m/n/10 citation
(auto = TRUE)\T1/ptm/m/n/10 ).
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[]\T1/ptm/m/n/10 Full doc-u-men-ta-tion and de-mos: [][]$\T1/zi4/m/n/10 http :
/ / yihui . name / knitr/$[][]\T1/ptm/m/n/10 ; FAQ's: [][]$\T1/zi4/m/n/10 http
: / / bit . ly / knitr-[]faq$[][]
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\T1/ptm/m/n/10 you gen-er-ate \T1/zi4/m/n/10 raw_output() \T1/ptm/m/n/10 to the
Mark-down out-put. In the pre-processor, you can \T1/zi4/m/n/10 extract_raw_ou
tput()
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 my-figure/\T1/ptm/m/n/10 ', you are not rec-om-m
ended to use hard-coded fig-ure paths like `\T1/zi4/m/n/10 \includegraphics{my-
figure/foo-1.pdf}\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 stead, you should use `\T1/zi4/m/n/10 \Sexpr{fig_chunk(\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )}\T1/ptm/m/n/10 ' or `\T1/zi4/
m/n/10 ![](\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r fig_chunk(\TS1/zi4/m/n/10 '\T1/zi4
/m/n/10 foo\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 , \TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pn
g\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 )\T1/ptm/m/n/
10 '.
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[]\T1/ptm/m/n/10 These hooks are mainly for the pack-age op-tion \T1/zi4/m/n/10
animation.fun\T1/ptm/m/n/10 , e.g. you can set \T1/zi4/m/n/10 opts_knit$set(an
imation.fun = hook_scianimator)\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Depending on the op-tions passed over, \T1/zi4/m/n/10 hook_plo
t_tex \T1/ptm/m/n/10 may re-turn the nor-mal `\T1/zi4/m/n/10 \includegraphics{}
\T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 many other op-tions into con-sid-er-a-tion to align plots and se
t fig-ure sizes, etc. Sim-i-larly, \T1/zi4/m/n/10 hook_plot_html\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 cal im-age files to Imgur, e.g. set the pack-age op-tion \T1/zi4
/m/n/10 opts_knit$set(upload.fun = imgur_upload)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 you want to write `\TS1/zi4/m/n/10 `\T1/zi4/m/n/10 r 1+1\TS1/zi4
/m/n/10 `\T1/ptm/m/n/10 ' lit-er-ally in an R Mark-down doc-u-ment, you may wri
te `\TS1/zi4/m/n/10 `` `\T1/zi4/m/n/10 r knitr::inline_expr(\TS1/zi4/m/n/10 '\T
1/zi4/m/n/10 1+1\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )\TS1/zi4/m/n/10 `
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[]\T1/zi4/m/n/10 kable(x, format, digits = getOption("digits"), row.names = NA
, col.names = NA, align,[]

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[]\T1/ptm/m/n/10 a list of ar-gu-ments to be passed to [][]\T1/zi4/m/n/10 forma
t[][][]() \T1/ptm/m/n/10 to for-mat ta-ble val-ues, e.g. \T1/zi4/m/n/10 list(bi
g.mark = \TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )
[23]
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[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 https : / / github . com / yihui / kni
tr-[]examples / blob / master / 091-[]knitr-[]table . Rnw$[][] \T1/ptm/m/n/10 f
or some
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[]\T1/ptm/m/n/10 The ar-gu-ments \T1/zi4/m/n/10 input \T1/ptm/m/n/10 and \T1/zi
4/m/n/10 output \T1/ptm/m/n/10 do not have to be re-stricted to files; they can
be \T1/zi4/m/n/10 stdin()\T1/ptm/m/n/10 /\T1/zi4/m/n/10 stdout()
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[]\T1/zi4/m/n/10 knit2html(input, output = NULL, ..., envir = parent.frame(),
text = NULL, quiet = FALSE,[]
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[]\T1/zi4/m/n/10 knit2pdf(input, output = NULL, compiler = NULL, envir = paren
t.frame(), quiet = FALSE,[]
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[]\T1/ptm/m/n/10 a log-i-cal vec-tor of length 2: whether to use the short-code
`\T1/zi4/m/n/10 [sourcecode lang=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 lang\TS1/zi4/
m/n/10 '\T1/zi4/m/n/10 ]\T1/ptm/m/n/10 '
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[]\T1/ptm/m/n/10 The en-gine func-tion has one ar-gu-ment \T1/zi4/m/n/10 option
s\T1/ptm/m/n/10 : the source code of the cur-rent chunk is in \T1/zi4/m/n/10 op
tions$code\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 case we can pass it through the \T1/zi4/m/n/10 engine.path \T1/p
tm/m/n/10 op-tion. For ex-am-ple, \T1/zi4/m/n/10 engine=\TS1/zi4/m/n/10 '\T1/zi
4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.path=\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 /usr/bin/ruby1.9.1\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 Ad-di-tional com-mand line ar-gu-ments can be passed through \T1
/zi4/m/n/10 options$engine.opts\T1/ptm/m/n/10 , e.g. \T1/zi4/m/n/10 engine=\TS1
/zi4/m/n/10 '\T1/zi4/m/n/10 ruby\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 ,engine.opts=\T
S1/zi4/m/n/10 '\T1/zi4/m/n/10 -v\TS1/zi4/m/n/10 '\T1/ptm/m/n/10 .
[33]
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[]\T1/ptm/m/n/10 Usage: [][]$\T1/zi4/m/n/10 http : / / yihui . name / knitr / o
bjects$[][]\T1/ptm/m/n/10 ; ex-am-ples: [][]$\T1/zi4/m/n/10 http : / / yihui .
name / knitr / demo / engines/$[][]
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[]\T1/zi4/m/n/10 knit_expand(file, ..., text = readLines(file, warn = FALSE),
delim = c("{{", "}}"))[]
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[]\T1/ptm/m/n/10 It re-turns the \T1/zi4/m/n/10 envir \T1/ptm/m/n/10 ar-gu-ment
of [][]\T1/zi4/m/n/10 knit[][][]\T1/ptm/m/n/10 , e.g. if we call [][]\T1/zi4/m
/n/10 knit[][][]() \T1/ptm/m/n/10 in the global en-vi-ron-ment, \T1/zi4/m/n/10
knit_global()
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[]\T1/ptm/m/n/10 It is rec-om-mended to leave a \T1/zi4/m/n/10 ... \T1/ptm/m/n/
10 ar-gu-ment in your method, to al-low fu-ture changes of the \T1/zi4/m/n/10 k
nit_print()
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[]\T1/ptm/m/n/10 the path of the cache database (nor-mally set in the global ch
unk op-tion \T1/zi4/m/n/10 cache.path\T1/ptm/m/n/10 )

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[]\T1/ptm/m/n/10 whether to [][]\T1/zi4/m/n/10 lazyLoad[][][] \T1/ptm/m/n/10 th
e cache database (de-pend-ing on the chunk op-tion \T1/zi4/m/n/10 cache.lazy =
TRUE
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[]\T1/ptm/m/n/10 Normally we set up the global op-tions once in the first code
chunk in a doc-u-ment us-ing \T1/zi4/m/n/10 opts_chunk$set()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 PDFCrop: [][]$\T1/zi4/m/n/10 https : / / www . ctan . org / pk
g / pdfcrop$[][]\T1/ptm/m/n/10 ; the \T1/zi4/m/n/10 convert \T1/ptm/m/n/10 com-
mand in Im-ageMag-ick: [][]$\T1/zi4/m/n/10 http :
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[]\T1/zi4/m/n/10 read_chunk(path, lines = readLines(path, warn = FALSE), label
s = NULL, from = NULL,[]
[55]
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[]\T1/ptm/m/n/10 Yihui Xie; the idea of the sec-ond ap-proach came from Pe-ter
Ruck-de-schel (au-thor of the \T1/ptm/b/n/10 SweaveListingUtils
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[]\T1/ptm/m/n/10 There are three vari-ants of mark-down doc-u-ments: or-di-nary
mark-down (\T1/zi4/m/n/10 render_markdown(strict = TRUE)\T1/ptm/m/n/10 ),

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\T1/ptm/m/n/10 ex-tended mark-down (e.g. GitHub Fla-vored Mark-down and pan-doc
; \T1/zi4/m/n/10 render_markdown(strict = FALSE)\T1/ptm/m/n/10 ),
[58]
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[]\T1/ptm/m/n/10 Jekyll and Liq-uid: [][]$\T1/zi4/m/n/10 https : / / github . c
om / jekyll / jekyll / wiki / Liquid-[]Extensions$[][]\T1/ptm/m/n/10 ; pret-tif
y.js:
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[]\T1/zi4/m/n/10 stitch(script, template = system.file("misc", "knitr-template
.Rnw", package = "knitr"),[]
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[]\T1/ptm/m/n/10 The pseudo com-mand `\T1/zi4/m/n/10 \SweaveInput{file.Rnw}\T1/
ptm/m/n/10 ' is con-verted to a code chunk header \T1/zi4/m/n/10 < i4/m/n/10 '\T1/zi4/m/n/10 file.Rnw\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 >>=\T1/ptm/m/
n/10 .

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[]\T1/ptm/m/n/10 Similarly `\T1/zi4/m/n/10 \SweaveOpts{opt = value}\T1/ptm/m/n/
10 ' is con-verted to a code chunk `\T1/zi4/m/n/10 opts_chunk$set(opt = value)\
T1/ptm/m/n/10 '

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\T1/ptm/m/n/10 mat-i-cally gen-er-ated); \T1/zi4/m/n/10 fig=FALSE \T1/ptm/m/n/1
0 is changed to \T1/zi4/m/n/10 fig.keep=\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 none\TS
1/zi4/m/n/10 '\T1/ptm/m/n/10 ; the de-vices \T1/zi4/m/n/10 pdf/jpeg/png/eps/tik
z=TRUE

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\T1/ptm/m/n/10 are con-verted to \T1/zi4/m/n/10 dev=\TS1/zi4/m/n/10 '\T1/zi4/m/
n/10 pdf\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 jpeg\T
S1/zi4/m/n/10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 png\TS1/zi4/m/n/
10 '\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 postscript\TS1/zi4/m/n/10 '
\T1/zi4/m/n/10 /\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 tikz\TS1/zi4/m/n/10 '\T1/ptm/m/
n/10 ; \T1/zi4/m/n/10 pdf/jpeg/png/eps/tikz=FALSE
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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 Suggests\T1/ptm/m/n/10 ' field of your `\T1/zi4/
m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file. Also make sure the ex-e-cuta-bles \T1/
zi4/m/n/10 pandoc \T1/ptm/m/n/10 and \T1/zi4/m/n/10 pandoc-citeproc

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\T1/zi4/m/n/10 which pandoc-citeproc \T1/ptm/m/n/10 in the ter-mi-nal (or \T1/z
i4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 pandoc\TS1/zi4/m/n/10 '\T1/
zi4/m/n/10 ) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 Sys.which(\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 pandoc-citeproc\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 )
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[]\T1/ptm/m/n/10 a pre-fix string for keys in Bib-TeX en-tries; by de-fault, it
is `\T1/zi4/m/n/10 R-\T1/ptm/m/n/10 ' un-less [][]\T1/zi4/m/n/10 option[][][](
\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 knitr.bib.prefix\TS1/zi4/m/n/10 '\T1/zi4/m/n/10
)

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[]\T1/ptm/m/n/10 The ci-ta-tion is forced to be gen-er-ated from the `\T1/zi4/m
/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file of the pack-age (\T1/zi4/m/n/10 citation
(auto = TRUE)\T1/ptm/m/n/10 ).
[70] (./Rd2.ind [71]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
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)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.option} has been referenced but does not exist, replaced by a fixed one

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t, replaced by a fixed one

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t, replaced by a fixed one

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, replaced by a fixed one

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t, replaced by a fixed one

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, replaced by a fixed one

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eplaced by a fixed one

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laced by a fixed one

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replaced by a fixed one

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, replaced by a fixed one

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replaced by a fixed one

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t, replaced by a fixed one

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s not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.markdownToHTML} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setwd} has been referenced but does not exist,
replaced by a fixed one

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eplaced by a fixed one

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st, replaced by a fixed one

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exist, replaced by a fixed one

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, replaced by a fixed one

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placed by a fixed one

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replaced by a fixed one

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t exist, replaced by a fixed one

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t exist, replaced by a fixed one

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exist, replaced by a fixed one

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ist, replaced by a fixed one

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exist, replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb> usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (73 pages, 256023 bytes).
Transcript written on Rd2.log.
Saving output to '/tmp/RtmpUmKsCI/Rbuild17dec9a6934/knitr/build/knitr.pdf' ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'knitr_1.15.20.tar.gz'

Distribution log

SVN checkout/GIT clone log


Build log for Windows 7 (R 3.0.x)

(knitr 1.4.4)
* installing to library 'z:/rforge/Rlib/win7-3.0'
ERROR: failed to lock directory 'z:/rforge/Rlib/win7-3.0' for modifying
Try removing 'z:/rforge/Rlib/win7-3.0/00LOCK-knitr'