r knit to pdf/html: pandoc document conversion failed with error 2

Question

The R Markdown file seems to work in Rstudio. The r Markdown file can be converted into word, but not pdf/html.(Yesterday it gave different problem, so I change my question here.) Any help will be appreciated!

This is the context of my Markdown file:

---
title: "Test"
author: "Test"
date: "2018/9/8"
output: html_document
---
## R test

```{r test}
x<-rnorm(500)
y<-rnorm(x*10)
ls()
plot(x,y)
rm(x,y)
```

This is an test.

This is the outcome is I knit to html:

 |......................                                           |  33%
  ordinary text without R code



processing file: test.Rmd
  |...........................................                      |  67%
label: test
  |.................................................................| 100%
  ordinary text without R code
/usr/local/bin/pandoc +RTS -K512m -RTS test.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /var/folders/_h/013l11r91m3gny4lqwsvh5qh0000gn/T//Rtmpfvxqld/rmarkdown-str268664475eb.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 
output file: test.knit.md

--smart/-S has been removed.  Use +smart or -smart extension instead.
For example: pandoc -f markdown+smart -t markdown-smart.
Try pandoc --help for more information.
error: pandoc document conversion failed with error 2
stop processing

This is the outcome if I knit to pdf:

|......................                                           |  33%
  ordinary text without R code

  |...........................................                      |  67%
label: test


processing file: test.Rmd
  |.................................................................| 100%
  ordinary text without R code

    /usr/local/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.pdf --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --variable graphics=yes --variable 'geometry:margin=1in' 
    output file: test.knit.md

    --latex-engine has been removed.  Use --pdf-engine instead.
    Try pandoc --help for more information.
    error: pandoc document conversion failed with error 2
    stop processing

Answer 1

A little background might help:

Pandoc is a Haskell binary (i.e. a distinct piece of non-R software), that is shipped with RStudio for sake of running RMarkdown conversion. It seems you are getting some deprecation warnings, like:

• --latex-engine has been removed. Use --pdf-engine instead.
• --smart/-S has been removed. Use +smart or -smart extension instead.

This tells me you probably have an older version of RStudio, thus an older version of Pandoc. You may want to reinstall RStudio to make sure you have the appropriate Pandoc version, then debug from there.

Also, make sure to reinstall knitr and rmarkdown with the newest versions.