I am writing an R package and would like to make a pdf reference manual of all functions in the package. I understood from here that R CMD check automatically c
I had the same issue. It seems that when you click Build or Check in Rstudio (when using devtools), by default arguments of '--no-manual' are added to the R CMD options.
I solved this by manually giving the arguments in the R command prompt:
library(devtools)
check(cleanup = FALSE,manual = TRUE,path = getwd())
# without running the examples
check(cleanup = FALSE,args = c('--no-examples'),manual = TRUE,path = getwd())
In this case, a folder called package.Rcheck will contain the manual as package-manual.pdf
Also check for any errors in the output during the check. There might be characters that might crash the documentation.