[R-pkg-devel] Macros in Rd files --- supplementary question.

It is more subtle than that.
\Sexpr triggers the creation of "partial Rd database" which becomes part of the built package (the tar.gz file), although what exactly happens may also depend on 'stage' options of the \Sexpr's.

... However when I do the "R CMD  build" thing, when it comes to the
"* building the PDF package manual"
step it says "Hmm ... looks like a package" (no shit, Sherlock!) and
emits a huge amount of verbose LaTeX diagnostics.

I have never seen  "* building the PDF package manual" from 'R CMD build', see below for a sample console output on Windows from a package which contains Rd macros and vignettes.

The messages you show seem to come from 'Rd2pdf'. Is it possible that you have some custom script that builds the manual, as well?

Usage: R CMD build [options] pkgdirs

Build R packages from package sources in the directories specified by
?pkgdirs?

Options:
   -h, --help        print short help message and exit
   -v, --version        print version info and exit

   --force               force removal of INDEX file
   --keep-empty-dirs     do not remove empty dirs
   --no-build-vignettes  do not (re)build package vignettes
   --no-manual           do not build the PDF manual even if \Sexprs are present
...
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