PDFs are missing images when compiling knitr .RNW examples

Question

I'm new to creating documents with knitr and Latex and I'm slowly being driven insane trying to figure out why the images of plots are missing from compiled pdfs.

For example, if I open the knitr minimal example that comes with the knitr package (v1.5) (stored in local R install directory .... \library\knitr\examples\knitr-minimal.Rnw) and compile it from within RStudio (version 0.98.490), I get a pdf file (saved here) that is missing the example images but otherwise correct.

Any ideas where I can look to track down what's causing this problem?

Session Info

> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> (1) LC_COLLATE=English_Ireland.1252  LC_CTYPE=English_Ireland.1252   
> (3) LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C                    
> (5) LC_TIME=English_Ireland.1252    
> 
> attached base packages:
> (1) stats     graphics  grDevices utils     datasets  methods   base     
> 
> loaded via a namespace (and not attached):
> (1) tools_3.0.2

Output from compiling the pdf in RStudio:

> grDevices::pdf.options(useDingbats = FALSE); utils::Sweave('knitr-minimal.Rnw', encoding='ISO8859-1')
>Writing to file knitr-minimal.tex
>Processing code chunks with options ...
> 1 : echo keep.source term verbatim (label = setup, knitr-minimal.Rnw:21)
> 2 : echo keep.source term verbatim (label = boring-random, knitr-minimal.Rnw:38)
> 3 : echo keep.source term verbatim (label = boring-plots, knitr-minimal.Rnw:47)
>
>You can now run (pdf)latex on 'knitr-minimal.tex'
>
>
>Running pdflatex.exe on knitr-minimal.tex...completed
>
>Created PDF: C:/Program Files/R/R-3.0.2/library/knitr/examples/knitr-minimal.pdf
>
>Issues: 1 warning

Horrendously long Latex Compilation Log

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>croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, ga
>lician, german, german-x-2012-05-30, greek, gujarati, hindi, hungarian, iceland
>ic, indonesian, interlingua, irish, italian, kannada, kurmanji, latin, latvian,
> lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek, ngerman, n
>german-x-2012-05-30, nynorsk, oriya, panjabi, pinyin, polish, portuguese, roman
>ian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, swissgerm
>an, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian, usengl
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>

Answer 1

In RStudio, the default weave option needs to be changed from Sweave to knitr. In Windows 7, I select the Tools tab, global options tab, Sweave tab, and then change "Sweave" defalut to "knitr".