R help - May 2024 - R CMD check vs RStudio check

I am trying to figure out why checking my package is deleting my inst/doc/
directory when I do it in RStudio.  Along the way I've hit another puzzle.
In RStudio the check runs and is mostly OK, aside from the deletion.  But when I
try with vanilla R, the check fails almost immediately:
-------------------------powershell---------------------------
PS C:\Users\rdboylan\Documents\BP\pimex> & $R CMD check .
* using log directory 'C:/Users/rdboylan/Documents/BP/pimex/..Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2019 x64 (build 17763)
* using session charset: ISO8859-1
* checking for file './DESCRIPTION' ... ERROR
Required fields missing or empty:
  'Author' 'Maintainer'
* DONE

Status: 1 ERROR
See
  'C:/Users/rdboylan/Documents/BP/pimex/..Rcheck/00check.log'
for details.

PS C:\Users\rdboylan\Documents\BP\pimex> $R
C:\Program Files\R\R-4.3.3\bin\R.exe
---------------------------------------------------------------

The DESCRIPTION file includes
Authors at R: 
    utils::person("Ross", "Boylan",
    email = "ross.boylan at ucsf.edu",
    role = c("aut", "cre", "cph")
    )
but no separate Author or Maintainer field.

RStudio is using devtools::check; I don't know if it is doing anything extra
beyond that.

I expected that the various ways of running check would be similar, or at least
approve of the same DESCRIPTION file.  Can anyone help me understand what is
going on, and how I can isolate the source of my problem?

Initially the problem with the directory deletion appeared running check in
RStudio; I believe RStudio calls devtools::check, which I assume ultimately does
the equivalent of R CMD check. The build invokes a bootstrap.R script I wrote,
which in turn runs LyX. And I'm not sure which of these is responsible for
deleting the directory.  When I invoke bootstrap.R directly from RStudio LyX
runs and nothing is deleted.

R 4.3.3; RStudio 2023.12.1+402; Windows Server 2019 Standard v1809.

P.S. What's with the "..Rcheck" log directory, which appears
literally with the 2 dots?  Is this just MS-Windows getting confused and not
interpreting .. as the parent directory?

? Fri, 3 May 2024 19:45:08 +0000
"Boylan, Ross via R-help" <r-help at r-project.org> ?????:
> & $R CMD check .
> * checking for file './DESCRIPTION' ... ERROR
> Required fields missing or empty:
>   'Author' 'Maintainer'
You're checking a source package directory. This could work, but it's
much easier and more reliable to (1) build a source tarball using R CMD
build and (2) check the tarball. This is probably part of what
devtools::check() does. (It can also do a lot of other things pre-R CMD
build.)

The reason checking the source directory is failing is because it's R
CMD build that creates the necessary 'Author' and 'Maintainer'
fields
from Authors at R in your DESCRIPTION.
> P.S. What's with the "..Rcheck" log directory, which appears
> literally with the 2 dots?  Is this just MS-Windows getting confused
> and not interpreting .. as the parent directory?
"..Rcheck" is built from the argument of R CMD check . followed by
".Rcheck".

-- 
Best regards,
Ivan