I do all my package development with the build environment in RStudio (0.99.891). Historically, when I would run a package check, the resulting package.Rcheck directory would have a package-manual.pdf file, but within the past few months whenever I check a package the manual PDF no longer appears in my directory. I have not changed any of my check package options but continue to use --as-cran.
It seems RStudio has not updated their documentation yet online for how to customize build options so that's no help. After seeing this question on SO: After running R CMD Check, the mypackage.Rcheck directory with PDF manual disappeared, I double checked and "Cleanup output after successful R CMD Check" is unchecked.
In RStudio's outdated documentation they describe a --no-manual option, but maybe this is now the default?
How can I get the manual back? I like to look it over before submitting to CRAN to make sure there are no issues.
That --no-manual text is not actually part of RStudio but is rather the output when you run R CMD check --help at a system command line. Is it possible you are affected by this NEWS item in version 3.2.0?
"Building the manuals now requires texi2any from texinfo 5.1 or later. CRAN binary builds include the manuals, but by default builds from source will not, and they will be accessed from CRAN. See the comments in ‘src/gnuwin32/MkRules.dist’ for how to specify the location of texi2any."