Put figure directly into Knitr document (without s

Question

I am extending a question I recently posted here (Put figure directly into Knitr document (without saving file of it in folder)).

I am writing an R package that generates a .pdf file for users that outputs summarizations of data. I have a .Rnw script in the package (here, my MWE of it is called test.Rnw). The user can do:

1) knit("test.Rnw") to create a test.tex file
2) "pdflatex test.tex" to create the test.pdf summary output file.

The .Rnw file generates many images. Originally, these all got saved in the current directory. These images being saved to the directory (or maybe the .aux or .log files that get created upon calling pdflatex on the .tex file) just does not seem as tidy as it could be (since users must remember to delete these image files). Secondarily, I also worry that this untidiness may cause issues when scripts are run multiple time.

So, in my previous post, we improved the .Rnw file by saving the images to a temporary folder. I have been told the files in the temporary folder get deleted each time a new R session is opened. However, I still worry about certain things:

1) I feel I may need to insert a line, like the one on line 19:

system(sprintf("%s", paste0("rm -r ", temppath, "/*")))

to automatically delete the files in the temporary folder each time the .Rnw file is run (so that the images do not only get deleted each time R gets restarted). This will keep the current directory clean of the images, and the user will not have to remember to manually delete the images. However, I do not know if this "solution" will pass CRAN standards to have a line to delete files in the temporary folder. The reason is that it deletes files in the user's system, which could cause problems if other programs are writing files to the temporary folder. I feel I have read about CRAN not allowing files to be written/deleted from the user's computer for obvious reasons. How strict would CRAN be about such a practice? Is there a safe way to go about it?

2) If writing and deleting the image files in a temporary file will not work, what is another way to accomplish the same effect (run the script without having cumbersome image files created in the folder)? Is it possible to instead have the images directly embedded in the output file (not needing to be saved to any directory)? I am pretty sure this is not possible. However, I have been told it is possible to do so with .Rmd, and that I could convert my .Rnw to .Rmd. This may be difficult because the .Rnw file must follow certain formats (text and margins) for the correct output, and it is very long. Is it possible to make use of the .Rmd capability (of inserting images directly into the output) only for the chunks that generate images, without rewriting the entire .Rnw file?

Below is my MWE:

\documentclass[nohyper]{tufte-handout}
\usepackage{tabularx} 
\usepackage{longtable}

\setcaptionfont{% changes caption font characteristics
  \normalfont\footnotesize
  \color{black}% <-- set color here
}

\begin{document}

<<setup, echo=FALSE>>=
library(knitr)
library(xtable)
library(ggplot2)
# Specify directory for figure output in a temporary directory
temppath <- tempdir()
# Erase all files in this temp directory first?
#system(sprintf("%s", paste0("rm -r ", temppath, "/*")))
opts_chunk$set(fig.path = temppath)
@

<<diamondData, echo=FALSE, fig.env = "marginfigure", out.width="0.95\\linewidth", fig.cap = "The diamond dataset has varibles depth and price.",fig.lp="mar:">>=
print(qplot(depth,price,data=diamonds))
@

<<echo=FALSE,results='asis'>>=
myDF <- data.frame(a = rnorm(1:10), b = letters[1:10])
print(xtable(myDF, caption= 'This data frame shows ten random variables from the distribution and a corresponding letter', label='tab:dataFrame'), floating = FALSE, tabular.environment = "longtable", include.rownames=FALSE)
@

Figure \ref{mar:diamondData} shows the diamonds data set, with the
variables price and depth.Table \ref{tab:dataFrame} shows letters a through j
corresponding to a random variable from a normal distribution.

\end{document}