Rmd Fail to knit: Error: pandoc document conversion failed with error 99

[Jason.C]

Greetings,

I'm having trouble with knit to html.
The process works when the plot command is commented out. As soon as the plot command is included, knit fails. Any suggestions or guidance would be helpful.

Jason the #rstatsnewbie

Error messages

output file: knit_issues_28April2020.knit.md

File knit_issues_28April2020_files/figure-html/---> plots-1.png" width=“672” /></p>

</div>

<script>

// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
  $('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
  bootstrapStylePandocTables();
});

</script>

<!-- tabsets -->

<script>
$(document).ready(function () {
  window.buildTabsets( not found in resource path
Error: pandoc document conversion failed with error 99
Execution halted

MRE (NOTE: uncomment the plot command to generate the error)

---
title: "knit issues April 28, 2020"
author: "Jason"
date: "4/28/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

library(knitr)
library(kableExtra)
library(tidyverse)
library(reprex)
library(here)
here()
dr_here(show_reason = FALSE)

zq.dat <- structure(list(group = structure(c(1L, 1L, 1L, 1L, 1L, 
1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 2L, 2L, 2L), .Label = c("HC", 
"CLBP", "FM", "TRUE"), class = "factor"), sex = structure(c(1L, 
1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 
2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 
2L), .Label = c("Female", "Male"), class = "factor"), slpQual = c(0, 
1, 1, 1, 1, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 
2, 0, 2, 1, 1, 2, 1, 2, 1, 1, 0, 0, 1, 0, 2, 0, 0, 1, 1, 2, 1, 
1, 1, 2, 1, 0, 1, 0), slpLat = c(1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 
1, 2, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 2, 0, 1, 1, 1, 2, 0, 
2, 1, 1, 2, 1, 1, 0, 0, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 0), slpDur = c(1, 
0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 
1, 0, 2, 1, 1, 0, 1, 3, 1, 0, 1, 1, 2, 1, 2, 0, 0, 1, 2, 1, 0, 
1, 1, 1, 1, 1, 1, 0), slpEff = c(0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 
0, 0, 0, 3, 3, 0, 3, 1, 0, 0, 3, 0, 0, 3, 1, 3, 0, 1, 1, 3, 3, 
0, 3, 3, 1, 0, 2, 0, 0, 1, 3, 3, 3, 0, 3, 0, 0, 0, 1, 0), slpDist = c(1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1), slpMeds = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 3, 1, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 2, 1, 0, 0, 0, 0, 3, 0, 0), 
    slpDayFcn = c(0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 
    0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 
    0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1), psqi_Global = c(3, 
    3, 7, 3, 5, 4, 3, 4, 2, 6, 1, 4, 4, 6, 7, 1, 7, 5, 6, 4, 
    5, 2, 6, 4, 8, 6, 4, 5, 8, 12, 6, 4, 6, 7, 7, 4, 8, 1, 1, 
    8, 8, 11, 9, 5, 8, 5, 5, 7, 5, 2), ess_total = c(5, 5, 4, 
    7, 10, 2, 5, 5, 4, 9, 6, 10, 8, 9, 6, 8, 9, 3, 6, 10, 8, 
    10, 3, 0, 10, 6, 6, 6, 9, 6, 6, 4, 3, 5, 3, 6, 6, 5, 1, 1, 
    3, 11, 3, 8, 8, 4, 7, 8, 5, 11), bdi_total = c(0, 1, 1, 13, 
    5, 0, 1, 6, 0, 7, 0, 2, 0, 6, 0, 3, 1, 0, 0, 7, 12, 5, 7, 
    0, 2, 8, 1, 9, 12, 4, 1, 0, 0, 1, 1, 0, 25, 0, 0, 13, 1, 
    5, 2, 7, 1, 4, 22, 6, 12, 2), mcgill_total = c(0, 0, 0, 0, 
    0, 0, 9, 0, 0, 4, 0, 1, 0, 5, 0, 0, 0, 0, 0, 38, 34, 16, 
    0, 0, 0, 5, 2, 14, 0, 0, 0, 25, 0, 0, 21, 0, 9, 0, 0, 42, 
    12, 4, 3, 44, 10, 18, 50, 39, 42, 9), TIB = c(7, 7.5, 8.5, 
    8, 9.5, 8.5, 7.5, 8.5, 7.5, 7, 9, 8, 8, 32, 31, 8.5, 32, 
    8.5, 8.75, 8, 32, 8, 7.5, 32.25, 6, 30, 7.5, 9, 8.5, 9, 30.5, 
    9, 30, 31, 7.25, 7, 8, 7.5, 9, 9, 30.75, 30.5, 32, 6.5, 32, 
    7, 6, 7.75, 8.5, 8.5)), row.names = c(NA, 50L), class = "data.frame")

#		GROUP BY SEX INFORMATION
groups_x_sex <- zq.dat %>%
	group_by(group, sex) %>% 
	tally()

groups_x_sex %>% 
	kable(align = "c", padding = 4) %>% 
	kable_styling("striped", full_width = F) %>% 
	collapse_rows(columns = 1:2, valign = "top") %>% 
	row_spec(0, bold = T, color = "white", background = "#461B7E" )

#plot(zq.dat)

[Jason.C]

The error is a result of how the code chunk was written.
I included an 'arrow' (i.e., --->) in my code chunks to help with organizing the document outline (see below). While this didn’t produce any issues for Knit in other chunks; the inclusion of the 'arrow' in a chunk with a plot command will consistently fail.

Solution Do not include an 'arrow' (i.e., --->) in any code chunks.

Example of original code chunk

 
> ```{r --->  McGill, eval=TRUE, echo=FALSE, message=FALSE }

>```

Revised code chunk

 
> ```{r McGill, eval=TRUE, echo=FALSE, message=FALSE }

>```