It is seems that you don't have the correct versions of pandoc in your shiny server. You may use some new feature of pandoc that requires pandoc > 2. Currently, standard RStudio production include the 1.19 I think. The preview product (IDE for example) embedded the 2.x.x
You can check on the server the version that should be included with the shiny server install (not sure about the path... but somewhere)
/opt/shiny-server/ext/pandoc/pandoc --version
You may need to update or install a new version for this Rmd of yours. The pandoc executable can be chosen with Sys.getenv("RSTUDIO_PANDOC") if you have several versions
Hope it helps