rmarkdown:render in for loop throws ! Undefined control sequence. \@sharp ->\makecell

I created a R markdown document that takes a report ID number as a parameter and then uses that ID to query a database to pull all the information that goes into the report.
The report uses these libraries: "rmarkdown", "readxl", "dplyr", "Rblpapi", "tidyr", "lubridate", "stringr","knitr", "kableExtra", "RCurl", "XML", "RMySQL" and "webshot"

The report worked fine when I ran it by clicking the knit button in RStudio with a hardcoded report ID#. When I moved to a for loop and calling rmarkdown::render with the Rmd file as a parameter the report will only run once and then throws this error for an add_header_above() header.

! Undefined control sequence.
@sharp ->\makecell
[c]{A title header that spans 5 columns}

If I restart R and run it it will run 1 report again and then fail. I made sure I only load packages once by checking if they are already loaded using (.packages()). I need to make a few dozen of these reports so calling render from the for loop needs to work.

These are the parameters I am passing to the render function:

thisValue = rmarkdown::render("AReport.Rmd",
params = list(reportID = thisID),
output_format = "pdf_document")

Where is add_header_above() ? Is it from one of the *down package ?

Are you not changing the output document name ?

This seems related to a missing CTAN package which contains the command \makecell. What tool are you using for making your table ?

You could also try to render the file in a new session each time so that the rendering happens in a clean new environment

callr::r(function(ID) {
  params = list(reportID = ID),
  output_format = "pdf_document", 
  output_file = paste0("report-", ID, ".pdf"))
}, list(ID = thisID))

Something like that (I don't have an example to try on.

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.