unable to output to pdf via knitR

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Mike Dylan

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Jun 14, 2017, 1:18:06 PM6/14/17

to knitr

I have this markdown and I need to output it to pdf file:

---
title: "Colors of xtable cells"
header-includes:
   - \usepackage{longtable}
   - \usepackage[table]{xcolor}
   - \usepackage{colortbl}
   - \usepackage{utf8}{inputenc}
output:
    pdf_document:
      latex_engine: xelatex
---

Build the example data set

```{r, include = FALSE}
library(xtable)
library(rmarkdown)
j <-
structure(list(Trans = c(89.8, 3337, NA, 97.55, NA, 3558.7, NA,
4290.6, NA, 65.95, 94.55, 3495.9), `%CPU` = c(6.938, 79.853,
1.875, 4.87, 1.46, 37.885, 1.63, 64.576, 1.165, 3.425, 5.67,
33.856), `%Heap Used` = c(9.9, 76.95, 3.77, 9.8, 6.73, 59.23,
3.94, 67.38, 3.73, 9.13, 9.57, 62.11), `Heap Usage/MB` = c(263.884,
1942.246, 99.104, 257.717, 178.951, 1657.447, 99.933, 2137.134,
96.687, 242.024, 256.302, 1646.117)), .Names = c("Trans", "%CPU",
"%Heap Used", "Heap Usage/MB"), class = "data.frame", row.names = c(NA,
-12L))
```

Create a version of the `data.frame` with red cells for \%CPU greater than 70.
Set the color and round to two digits.

```{r, include = FALSE}
j[, 2] <- ifelse(j[, 2] > 70, paste("\\cellcolor{red}{", round(j[, 2], 2), "}"), round(j[, 2], 2))
```

The resulting table is:

```{r results = "asis"}
print(xtable(j,
             digits = 2,
             row.names = FALSE,
             caption = "JVM Usage"),
      sanitize.text.function = identity,
      sanitize.colnames.function = NULL,
      caption.placement   = "top",
      tabular.environment = "longtable",
      comment = FALSE,
      floating=FALSE)
```

I keep getting this error:

! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.1 < pandoc.exe: Error producing PDF from TeX source Error: pandoc document conversion failed with error 43 In addition: Warning message: running command '"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS test_color.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test_color.pdf --template "C:\Documents\R\win-library\3.2\rmarkdown\rmd\latex\default.tex" --highlight-style tango --latex-engine xelatex --variable graphics=yes --variable "geometry:margin=1in"' had status 43 Execution halted