R create reference manual with R CMD check

Question

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 creates a reference manual.

Here I read that a manual entry is created "of the functions you listed in the export section of NAMESPACE".

My NAMESPACE file looks as follows:

# Export all names
exportPattern(".")

# Import all packages listed as Imports or Depends
import(
  LIM
)

so I thought everything will be exported. During R CMD check on the package directory, at the very end it says:

 * checking PDF version of manual ... OK

However, I do not find a reference manual in my package directory (I would assume it would be in inst/doc). What am I missing here?

Blaeberry

Answer 1

R CMD check creates a directory PACKAGE.RCheck. In this directory you could find the file PACKAGE-manual.pdf.

Injunction

The PACKAGE-manual.pdf is located one folder above the package directory, in ../package.Rcheck. – Oakes

Answer 2

Another way is to create the reference manual directly using:

R CMD Rd2pdf mypackage

where mypackage is the folder containing your R package code folder structure including the man folder with your .Rd files.

For some reason I never get the reference manual during build or check in RStudio, maybe because I've missed a setting somewhere. But running the command like this works fine as well.

Humidify

Just tried it, it works well! Thanks for pointing out Rd2pdf! – Blaeberry

Same problem as above, solved thanks to your suggestion. I really do not understand why Rstudio messes up so much. – Silsby

While this is useful, it has a feature (?) that it does not respect .Rbuildignore – Chainman

Answer 3

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.

Blastocyst

see RStudio preferences to change this easily – Surtout

Answer 4

Another workaround is to produce it with:

build_manual(path=getwd())
#or
check(manual = TRUE, args="--output=~/folder/subfolder")

Faraway