I have an RMarkdown file open in RStudio Server v1.0.136. I typically compile to HTML format, so I have the YAML header set for this. However, if I try to compile to PDF instead, the Rstudio messes up the YAML and breaks the document.
The header goes from this:
---
title: "NGS580 Analysis Report"
author: '`r Sys.info()[["user"]] `'
date: '`r format(Sys.time(), "%B %d, %Y")`'
output:
html_document:
toc: yes
df_print: paged
keep_md: yes
css: styles.css
number_sections: yes
params:
child: !r c("flagstat.Rmd", "haplotypecaller.Rmd", "lofreq.Rmd", "sample-coverage.Rmd")
input_dir: input
---
to this:
---
title: "NGS580 Analysis Report"
author: '`r Sys.info()[["user"]] `'
date: '`r format(Sys.time(), "%B %d, %Y")`'
output:
pdf_document:
toc: yes
html_document:
css: styles.css
df_print: paged
keep_md: yes
number_sections: yes
toc: yes
params:
child: c("flagstat.Rmd", "haplotypecaller.Rmd", "lofreq.Rmd", "sample-coverage.Rmd")
input_dir: input
---
Note that among other things, the R expression in the parameters has lost the leading !r which makes it work. It also re-arranges the order of the entries (inconseqential), and in one case it also broke the quoting of the R expressions I am using in my author and date field.
Here is a gif of it in action:
