[R] R CMD check vs RStudio check

[Boylan, Ross]

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 using R: 
    utils::person("Ross", "Boylan",
    email = "ross.boylan using 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?